X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fenergy.f90;h=ac1202871443616851aa948f8c764d29a98e4a6f;hb=dc956ab7ea5a327e869c9671337d951a55c2535b;hp=77c46dd51d150c7f8657f6f521db325a1decc8b8;hpb=9bed09ef53885a28392d806dee8108c48a7cef9d;p=unres4.git diff --git a/source/unres/energy.f90 b/source/unres/energy.f90 index 77c46dd..ac12028 100644 --- a/source/unres/energy.f90 +++ b/source/unres/energy.f90 @@ -39,60 +39,61 @@ ! Change 12/1/95 - common block CONTACTS1 included. ! common /contacts1/ - integer,dimension(:),allocatable :: num_cont !(maxres) - integer,dimension(:,:),allocatable :: jcont !(maxconts,maxres) - real(kind=8),dimension(:,:),allocatable :: facont,ees0plist !(maxconts,maxres) - real(kind=8),dimension(:,:,:),allocatable :: gacont !(3,maxconts,maxres) + integer,dimension(:),allocatable :: num_cont !(maxres) + integer,dimension(:,:),allocatable :: jcont !(maxconts,maxres) + real(kind=8),dimension(:,:),allocatable :: facont,ees0plist !(maxconts,maxres) + real(kind=8),dimension(:,:,:),allocatable :: gacont !(3,maxconts,maxres) integer,dimension(:),allocatable :: ishield_list integer,dimension(:,:),allocatable :: shield_list + real(kind=8),dimension(:),allocatable :: enetube,enecavtube ! ! 12/26/95 - H-bonding contacts ! common /contacts_hb/ real(kind=8),dimension(:,:,:),allocatable :: gacontp_hb1,gacontp_hb2,& - gacontp_hb3,gacontm_hb1,gacontm_hb2,gacontm_hb3,gacont_hbr,grij_hb_cont !(3,maxconts,maxres) + gacontp_hb3,gacontm_hb1,gacontm_hb2,gacontm_hb3,gacont_hbr,grij_hb_cont !(3,maxconts,maxres) real(kind=8),dimension(:,:),allocatable :: facont_hb,ees0p,& - ees0m,d_cont !(maxconts,maxres) - integer,dimension(:),allocatable :: num_cont_hb !(maxres) - integer,dimension(:,:),allocatable :: jcont_hb !(maxconts,maxres) + ees0m,d_cont !(maxconts,maxres) + integer,dimension(:),allocatable :: num_cont_hb !(maxres) + integer,dimension(:,:),allocatable :: jcont_hb !(maxconts,maxres) ! 9/23/99 Added improper rotation matrices and matrices of dipole-dipole ! interactions ! 7/25/08 commented out; not needed when cumulants used ! Interactions of pseudo-dipoles generated by loc-el interactions. ! common /dipint/ real(kind=8),dimension(:,:,:),allocatable :: dip,& - dipderg !(4,maxconts,maxres) + dipderg !(4,maxconts,maxres) real(kind=8),dimension(:,:,:,:,:),allocatable :: dipderx !(3,5,4,maxconts,maxres) ! 10/30/99 Added other pre-computed vectors and matrices needed ! to calculate three - six-order el-loc correlation terms ! common /rotat/ - real(kind=8),dimension(:,:,:),allocatable :: Ug,Ugder,Ug2,Ug2der !(2,2,maxres) + real(kind=8),dimension(:,:,:),allocatable :: Ug,Ugder,Ug2,Ug2der !(2,2,maxres) real(kind=8),dimension(:,:),allocatable :: obrot,obrot2,obrot_der,& - obrot2_der !(2,maxres) + obrot2_der !(2,maxres) ! ! This common block contains vectors and matrices dependent on a single ! amino-acid residue. ! common /precomp1/ real(kind=8),dimension(:,:),allocatable :: mu,muder,Ub2,Ub2der,& - Ctobr,Ctobrder,Dtobr2,Dtobr2der !(2,maxres) + Ctobr,Ctobrder,Dtobr2,Dtobr2der !(2,maxres) real(kind=8),dimension(:,:,:),allocatable :: EUg,EUgder,CUg,& - CUgder,DUg,Dugder,DtUg2,DtUg2der !(2,2,maxres) + CUgder,DUg,Dugder,DtUg2,DtUg2der !(2,2,maxres) ! This common block contains vectors and matrices dependent on two ! consecutive amino-acid residues. ! common /precomp2/ real(kind=8),dimension(:,:),allocatable :: Ug2Db1t,Ug2Db1tder,& - CUgb2,CUgb2der !(2,maxres) + CUgb2,CUgb2der !(2,maxres) real(kind=8),dimension(:,:,:),allocatable :: EUgC,EUgCder,& - EUgD,EUgDder,DtUg2EUg,Ug2DtEUg !(2,2,maxres) + EUgD,EUgDder,DtUg2EUg,Ug2DtEUg !(2,2,maxres) real(kind=8),dimension(:,:,:,:),allocatable :: Ug2DtEUgder,& - DtUg2EUgder !(2,2,2,maxres) + DtUg2EUgder !(2,2,2,maxres) ! common /rotat_old/ real(kind=8),dimension(:),allocatable :: costab,sintab,& - costab2,sintab2 !(maxres) + costab2,sintab2 !(maxres) ! This common block contains dipole-interaction matrices and their ! Cartesian derivatives. ! common /dipmat/ - real(kind=8),dimension(:,:,:,:),allocatable :: a_chuj !(2,2,maxconts,maxres) - real(kind=8),dimension(:,:,:,:,:,:),allocatable :: a_chuj_der !(2,2,3,5,maxconts,maxres) + real(kind=8),dimension(:,:,:,:),allocatable :: a_chuj !(2,2,maxconts,maxres) + real(kind=8),dimension(:,:,:,:,:,:),allocatable :: a_chuj_der !(2,2,3,5,maxconts,maxres) ! common /diploc/ real(kind=8),dimension(2,2,2) :: AEA,AEAderg,EAEA,AECA,& AECAderg,ADtEA,ADtEA1,AEAb1,AEAb1derg,AEAb2 @@ -123,16 +124,30 @@ gshieldc_ec,gshieldc_loc_ec,gshieldx_t3, & gshieldc_t3,gshieldc_loc_t3,gshieldx_t4,gshieldc_t4, & gshieldc_loc_t4,gshieldx_ll,gshieldc_ll,gshieldc_loc_ll,& - grad_shield !(3,maxres) + grad_shield,gg_tube,gg_tube_sc,gradafm !(3,maxres) +!-----------------------------NUCLEIC GRADIENT + real(kind=8),dimension(:,:),allocatable ::gradb_nucl,gradbx_nucl, & + gvdwpsb1,gelpp,gvdwpsb,gelsbc,gelsbx,gvdwsbx,gvdwsbc,gsbloc,& + gsblocx,gradcorr_nucl,gradxorr_nucl,gradcorr3_nucl,gradxorr3_nucl,& + gvdwpp_nucl +!-----------------------------NUCLEIC-PROTEIN GRADIENT + real(kind=8),dimension(:,:),allocatable :: gvdwx_scbase,gvdwc_scbase,& + gvdwx_pepbase,gvdwc_pepbase,gvdwx_scpho,gvdwc_scpho,& + gvdwc_peppho +!------------------------------IONS GRADIENT + real(kind=8),dimension(:,:),allocatable :: gradcatcat, & + gradpepcat,gradpepcatx ! real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2) + + real(kind=8),dimension(:,:),allocatable :: gel_loc,gel_loc_long,& gcorr3_turn,gcorr4_turn,gcorr6_turn,gradb,gradbx !(3,maxres) real(kind=8),dimension(:),allocatable :: gel_loc_loc,& gel_loc_turn3,gel_loc_turn4,gel_loc_turn6,gcorr_loc,g_corr5_loc,& - g_corr6_loc !(maxvar) + g_corr6_loc !(maxvar) real(kind=8),dimension(:,:),allocatable :: gsccorc,gsccorx !(3,maxres) - real(kind=8),dimension(:),allocatable :: gsccor_loc !(maxres) -! real(kind=8),dimension(:,:,:),allocatable :: dtheta !(3,2,maxres) + real(kind=8),dimension(:),allocatable :: gsccor_loc !(maxres) +! real(kind=8),dimension(:,:,:),allocatable :: dtheta !(3,2,maxres) real(kind=8),dimension(:,:),allocatable :: gscloc,gsclocx !(3,maxres) ! real(kind=8),dimension(:,:,:),allocatable :: dphi,dalpha,domega !(3,3,maxres) real(kind=8),dimension(:,:,:),allocatable :: grad_shield_side, & @@ -144,7 +159,7 @@ ! common /deriv_scloc/ real(kind=8),dimension(:,:),allocatable :: dXX_C1tab,dYY_C1tab,& dZZ_C1tab,dXX_Ctab,dYY_Ctab,dZZ_Ctab,dXX_XYZtab,dYY_XYZtab,& - dZZ_XYZtab !(3,maxres) + dZZ_XYZtab !(3,maxres) !----------------------------------------------------------------------------- ! common.maxgrad ! common /maxgrad/ @@ -162,7 +177,7 @@ ! common /qmeas/ real(kind=8) :: Ucdfrag,Ucdpair real(kind=8),dimension(:,:),allocatable :: dUdconst,dUdxconst,& - dqwol,dxqwol !(3,0:MAXRES) + dqwol,dxqwol !(3,0:MAXRES) !----------------------------------------------------------------------------- ! common.sbridge ! common /dyn_ssbond/ @@ -172,7 +187,7 @@ ! Parameters of the SCCOR term ! common/sccor/ real(kind=8),dimension(:,:,:,:),allocatable :: dcostau,dsintau,& - dcosomicron,domicron !(3,3,3,maxres2) + dcosomicron,domicron !(3,3,3,maxres2) !----------------------------------------------------------------------------- ! common.vectors ! common /vectors/ @@ -180,7 +195,8 @@ real(kind=8),dimension(:,:,:,:),allocatable :: uygrad,uzgrad !(3,3,2,maxres) !----------------------------------------------------------------------------- ! common /przechowalnia/ - real(kind=8),dimension(:,:,:),allocatable :: zapas !(max_dim,maxconts,max_fg_procs) + real(kind=8),dimension(:,:,:),allocatable :: zapas + real(kind=8),dimension(:,:,:,:),allocatable ::zapas2 !(max_dim,maxconts,max_fg_procs) real(kind=8),dimension(:,:,:),allocatable :: fromto !(3,3,maxdim)(maxdim=(maxres-1)*(maxres-2)/2) !----------------------------------------------------------------------------- !----------------------------------------------------------------------------- @@ -222,8 +238,17 @@ integer :: n_corr,n_corr1,ierror real(kind=8) :: etors,edihcnstr,etors_d,esccor,ehpb real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,escloc,ees,eel_loc - real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran + real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran,etube, & + Eafmforce,ethetacnstr real(kind=8) :: ecorr,ecorr5,ecorr6,eturn6 +! now energies for nulceic alone parameters + real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,& + ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,& + ecorr3_nucl +! energies for ions + real(kind=8) :: ecation_prot,ecationcation +! energies for protein nucleic acid interaction + real(kind=8) :: escbase,epepbase,escpho,epeppho #ifdef MPI real(kind=8) :: weights_(n_ene) !,time_Bcast,time_Bcastw @@ -264,6 +289,27 @@ weights_(17)=wbond weights_(18)=scal14 weights_(21)=wsccor + weights_(26)=wvdwpp_nucl + weights_(27)=welpp + weights_(28)=wvdwpsb + weights_(29)=welpsb + weights_(30)=wvdwsb + weights_(31)=welsb + weights_(32)=wbond_nucl + weights_(33)=wang_nucl + weights_(34)=wsbloc + weights_(35)=wtor_nucl + weights_(36)=wtor_d_nucl + weights_(37)=wcorr_nucl + weights_(38)=wcorr3_nucl + weights_(41)=wcatcat + weights_(42)=wcatprot + weights_(46)=wscbase + weights_(47)=wscpho + weights_(48)=wpeppho +! wcatcat= weights(41) +! wcatprot=weights(42) + ! FG Master broadcasts the WEIGHTS_ array call MPI_Bcast(weights_(1),n_ene,& MPI_DOUBLE_PRECISION,king,FG_COMM,IERROR) @@ -290,6 +336,24 @@ wbond=weights(17) scal14=weights(18) wsccor=weights(21) + wvdwpp_nucl =weights(26) + welpp =weights(27) + wvdwpsb=weights(28) + welpsb =weights(29) + wvdwsb =weights(30) + welsb =weights(31) + wbond_nucl =weights(32) + wang_nucl =weights(33) + wsbloc =weights(34) + wtor_nucl =weights(35) + wtor_d_nucl =weights(36) + wcorr_nucl =weights(37) + wcorr3_nucl =weights(38) + wcatcat= weights(41) + wcatprot=weights(42) + wscbase=weights(46) + wscpho=weights(47) + wpeppho=weights(48) endif time_Bcast=time_Bcast+MPI_Wtime()-time00 time_Bcastw=time_Bcastw+MPI_Wtime()-time00 @@ -307,7 +371,7 @@ #endif ! ! Compute the side-chain and electrostatic interaction energy - print *, "Before EVDW" +! print *, "Before EVDW" ! goto (101,102,103,104,105,106) ipot select case(ipot) ! Lennard-Jones potential. @@ -355,6 +419,7 @@ if (shield_mode.eq.2) then call set_shield_fac2 endif +! print *,"AFTER EGB",ipot,evdw !mc !mc Sep-06: egb takes care of dynamic ss bonds too !mc @@ -370,7 +435,7 @@ ! print *,"Processor",myrank," left VEC_AND_DERIV" if (ipot.lt.6) then #ifdef SPLITELE - print *,"after ipot if", ipot +! print *,"after ipot if", ipot if (welec.gt.0d0.or.wvdwpp.gt.0d0.or.wel_loc.gt.0d0.or. & wturn3.gt.0d0.or.wturn4.gt.0d0 .or. wcorr.gt.0.0d0 & .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.d0 & @@ -420,6 +485,7 @@ ! Calculate the bond-stretching energy ! call ebond(estr) +! print *,"EBOND",estr ! write(iout,*) "in etotal afer ebond",ipot ! @@ -433,9 +499,10 @@ ! Calculate the virtual-bond-angle energy. ! if (wang.gt.0d0) then - call ebend(ebe) + call ebend(ebe,ethetacnstr) else ebe=0 + ethetacnstr=0 endif ! print *,"Processor",myrank," computed UB" ! @@ -520,7 +587,40 @@ else eliptran=0.0d0 endif - + if (fg_rank.eq.0) then + if (AFMlog.gt.0) then + call AFMforce(Eafmforce) + else if (selfguide.gt.0) then + call AFMvel(Eafmforce) + endif + endif + if (tubemode.eq.1) then + call calctube(etube) + else if (tubemode.eq.2) then + call calctube2(etube) + elseif (tubemode.eq.3) then + call calcnano(etube) + else + etube=0.0d0 + endif +!-------------------------------------------------------- +! print *,"before",ees,evdw1,ecorr + call ebond_nucl(estr_nucl) + call ebend_nucl(ebe_nucl) + call etor_nucl(etors_nucl) + call esb_gb(evdwsb,eelsb) + call epp_nucl_sub(evdwpp,eespp) + call epsb(evdwpsb,eelpsb) + call esb(esbloc) + call multibody_hb_nucl(ecorr_nucl,ecorr3_nucl,n_corr,n_corr1) + call ecatcat(ecationcation) + call ecat_prot(ecation_prot) + call eprot_sc_base(escbase) + call epep_sc_base(epepbase) + call eprot_sc_phosphate(escpho) + call eprot_pep_phosphate(epeppho) +! call ecatcat(ecationcation) +! print *,"after ebend", ebe_nucl #ifdef TIMING time_enecalc=time_enecalc+MPI_Wtime()-time00 #endif @@ -563,9 +663,33 @@ energia(20)=Uconst+Uconst_back energia(21)=esccor energia(22)=eliptran + energia(23)=Eafmforce + energia(24)=ethetacnstr + energia(25)=etube +!--------------------------------------------------------------- + energia(26)=evdwpp + energia(27)=eespp + energia(28)=evdwpsb + energia(29)=eelpsb + energia(30)=evdwsb + energia(31)=eelsb + energia(32)=estr_nucl + energia(33)=ebe_nucl + energia(34)=esbloc + energia(35)=etors_nucl + energia(36)=etors_d_nucl + energia(37)=ecorr_nucl + energia(38)=ecorr3_nucl +!---------------------------------------------------------------------- ! Here are the energies showed per procesor if the are more processors ! per molecule then we sum it up in sum_energy subroutine ! print *," Processor",myrank," calls SUM_ENERGY" + energia(41)=ecation_prot + energia(42)=ecationcation + energia(46)=escbase + energia(47)=epepbase + energia(48)=escpho + energia(49)=epeppho call sum_energy(energia,.true.) if (dyn_ss) call dyn_set_nss ! print *," Processor",myrank," left SUM_ENERGY" @@ -604,7 +728,12 @@ real(kind=8) :: evdw,evdw2,evdw2_14,ees,evdw1,ecorr,ecorr5,ecorr6 real(kind=8) :: eel_loc,eello_turn3,eello_turn4,eturn6,ebe,escloc real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,esccor,etot, & - eliptran + eliptran,etube, Eafmforce,ethetacnstr + real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,& + ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,& + ecorr3_nucl + real(kind=8) :: ecation_prot,ecationcation + real(kind=8) :: escbase,epepbase,escpho,epeppho integer :: i #ifdef MPI integer :: ierr @@ -665,20 +794,60 @@ Uconst=energia(20) esccor=energia(21) eliptran=energia(22) + Eafmforce=energia(23) + ethetacnstr=energia(24) + etube=energia(25) + evdwpp=energia(26) + eespp=energia(27) + evdwpsb=energia(28) + eelpsb=energia(29) + evdwsb=energia(30) + eelsb=energia(31) + estr_nucl=energia(32) + ebe_nucl=energia(33) + esbloc=energia(34) + etors_nucl=energia(35) + etors_d_nucl=energia(36) + ecorr_nucl=energia(37) + ecorr3_nucl=energia(38) + ecation_prot=energia(41) + ecationcation=energia(42) + escbase=energia(46) + epepbase=energia(47) + escpho=energia(48) + epeppho=energia(49) +! energia(41)=ecation_prot +! energia(42)=ecationcation + + #ifdef SPLITELE etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 & +wang*ebe+wtor*etors+wscloc*escloc & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & - +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran + +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube& + +Eafmforce+ethetacnstr & + +wbond_nucl*estr_nucl+wang_nucl*ebe_nucl& + +wvdwpp_nucl*evdwpp+welpp*eespp+wvdwpsb*evdwpsb+welpsb*eelpsb& + +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl& + +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl& + +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase& + +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc & +wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 & +wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 & +wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d & - +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran + +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube& + +Eafmforce+ethetacnstr & + +wbond_nucl*estr_nucl+wang_nucl*ebe_nucl& + +wvdwpp_nucl*evdwpp+welpp*eespp+wvdwpsb*evdwpsb+welpsb*eelpsb& + +wvdwsb*evdwsb+welsb*eelsb+wsbloc*esbloc+wtor_nucl*etors_nucl& + +wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl& + +wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase& + +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho #endif energia(0)=etot ! detecting NaNQ @@ -801,7 +970,13 @@ !el local variables real(kind=8) :: etot,evdw,evdw2,ees,evdw1,ecorr,ecorr5,ecorr6,eel_loc real(kind=8) :: eello_turn6,eello_turn3,eello_turn4,ebe,escloc - real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran + real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran,& + etube,ethetacnstr,Eafmforce + real(kind=8) :: evdwpp,eespp,evdwpsb,eelpsb,evdwsb,eelsb,estr_nucl,& + ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,& + ecorr3_nucl + real(kind=8) :: ecation_prot,ecationcation + real(kind=8) :: escbase,epepbase,escpho,epeppho etot=energia(0) evdw=energia(1) @@ -832,7 +1007,28 @@ Uconst=energia(20) esccor=energia(21) eliptran=energia(22) - + Eafmforce=energia(23) + ethetacnstr=energia(24) + etube=energia(25) + evdwpp=energia(26) + eespp=energia(27) + evdwpsb=energia(28) + eelpsb=energia(29) + evdwsb=energia(30) + eelsb=energia(31) + estr_nucl=energia(32) + ebe_nucl=energia(33) + esbloc=energia(34) + etors_nucl=energia(35) + etors_d_nucl=energia(36) + ecorr_nucl=energia(37) + ecorr3_nucl=energia(38) + ecation_prot=energia(41) + ecationcation=energia(42) + escbase=energia(46) + epepbase=energia(47) + escpho=energia(48) + epeppho=energia(49) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,& estr,wbond,ebe,wang,& @@ -840,8 +1036,15 @@ ecorr,wcorr,& ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,& eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,& - edihcnstr,ebr*nss,& - Uconst,eliptran,wliptran,etot + edihcnstr,ethetacnstr,ebr*nss,& + Uconst,eliptran,wliptran,Eafmforce,etube,wtube, & ! till now protein + estr_nucl,wbond_nucl,ebe_nucl,wang_nucl, & + evdwpp,wvdwpp_nucl,eespp,welpp,evdwpsb,wvdwpsb,eelpsb,welpsb,& + evdwsb,wvdwsb,eelsb,welsb,esbloc,wsbloc,etors_nucl,wtor_nucl,& + etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,& + ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, & + escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,& + etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ & @@ -863,9 +1066,31 @@ 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & + 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST= ',1pE16.6,' (Constraint energy)'/ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/& + 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ & + 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ & + 'ESTR_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (stretching for nucleic)'/ & + 'EBE_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (bending for nucleic)'/ & + 'EVDW_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-phosphate VDW)'/ & + 'EESPP_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-phosphate elec)'/ & + 'EVDWPSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-sugarbase VDW)'/ & + 'EESPSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-sugarbase elec)'/ & + 'EVDWSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase-sugarbase VDW)'/ & + 'EESSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase-sugarbase elec)'/ & + 'ESBLOC_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase rotamer)'/ & + 'ETORS_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(torsional)'/ & + 'ETORSD_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(double torsional)'/ & + 'ECORR_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(multibody 4th order)'/ & + 'ECORR3_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(multibody 3th order)'/ & + 'ECATPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(cation prot)'/ & + 'ECATCAT=',1pE16.6,' WEIGHT=',1pD16.6,'(cation cation)'/ & + 'ESCBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-base)'/ & + 'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ & + 'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/& + 'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/& 'ETOT= ',1pE16.6,' (total)') #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,& @@ -874,7 +1099,15 @@ ecorr,wcorr,& ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,& eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,& - ebr*nss,Uconst,eliptran,wliptran,etot + ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, & + etube,wtube, & + estr_nucl,wbond_nucl, ebe_nucl,wang_nucl,& + evdwpp,wvdwpp_nucl,eespp,welpp,evdwpsb,wvdwpsb,eelpsb,welpsb& + evdwsb,wvdwsb,eelsb,welsb,esbloc,wsbloc,etors_nucl,wtor_nucl& + etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,& + ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, & + escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,& + etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ & @@ -895,9 +1128,31 @@ 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/ & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/ & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/ & + 'ETHETC= ',1pE16.6,' (valence angle constraints)'/ & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ & 'UCONST=',1pE16.6,' (Constraint energy)'/ & 'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ & + 'EAFM= ',1pE16.6,' (atomic-force microscopy)'/ & + 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ & + 'ESTR_nucl= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching for nucleic)'/ & + 'EBE_nucl=',1pE16.6,' WEIGHT=',1pD16.6,' (bending for nucleic)'/ & + 'EVDW_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-phosphate VDW)'/ & + 'EESPP_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-phosphate elec)'/ & + 'EVDWPSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-sugarbase VDW)'/ & + 'EESPSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(phosphate-sugarbase elec)'/ & + 'EVDWSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase-sugarbase VDW)'/ & + 'EESSB_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase-sugarbase elec)'/ & + 'ESBLOC_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(sugarbase rotamer)'/ & + 'ETORS_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(torsional)'/ & + 'ETORSD_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(double torsional)'/ & + 'ECORR_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(multibody 4th order)'/ & + 'ECORR3_nucl=',1pE16.6,' WEIGHT=',1pD16.6,'(multibody 3th order)'/ & + 'ECATPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(cation prot)'/ & + 'ECATCAT=',1pE16.6,' WEIGHT=',1pD16.6,'(cation cation)'/ & + 'ESCBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-base)'/ & + 'EPEPBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-base)'/ & + 'ESCPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(sc-prot nucl-phosphate)'/& + 'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/& 'ETOT= ',1pE16.6,' (total)') #endif return @@ -934,13 +1189,13 @@ evdw=0.0D0 ! allocate(num_cont(iatsc_s:iatsc_e)) !(maxres) nnt,nct-2 ! allocate(jcont(nres/4,iatsc_s:iatsc_e)) !(maxconts,maxres) (maxconts=maxres/4) -! allocate(facont(nres/4,iatsc_s:iatsc_e)) !(maxconts,maxres) -! allocate(gacont(3,nres/4,iatsc_s:iatsc_e)) !(3,maxconts,maxres) +! allocate(facont(nres/4,iatsc_s:iatsc_e)) !(maxconts,maxres) +! allocate(gacont(3,nres/4,iatsc_s:iatsc_e)) !(3,maxconts,maxres) do i=iatsc_s,iatsc_e - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -953,7 +1208,7 @@ !d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint), !d & 'iend=',iend(i,iint) do j=istart(i,iint),iend(i,iint) - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -970,7 +1225,7 @@ !d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) !d epsi=bb(itypi,itypj)**2/aa(itypi,itypj) !d write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)') -!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), +!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj), !d & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm, !d & (c(k,i),k=1,3),(c(k,j),k=1,3) evdw=evdw+evdwij @@ -1096,9 +1351,9 @@ ! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -1107,7 +1362,7 @@ ! do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -1125,7 +1380,7 @@ !d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) !d epsi=bb(itypi,itypj)**2/aa(itypi,itypj) !d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)') -!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), +!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj), !d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, !d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, !d & (c(k,i),k=1,3),(c(k,j),k=1,3) @@ -1197,9 +1452,9 @@ ! endif !el ind=0 do i=iatsc_s,iatsc_e - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -1214,7 +1469,7 @@ do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -1266,7 +1521,7 @@ sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) !d write (iout,'(2(a3,i3,2x),15(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & epsi,sigm,chi1,chi2,chip1,chip2, !d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq), !d & om1,om2,om12,1.0D0/dsqrt(rrij), @@ -1329,10 +1584,10 @@ !el ind=0 do i=iatsc_s,iatsc_e !C print *,"I am in EVDW",i - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) ! if (i.ne.47) cycle if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -1365,7 +1620,7 @@ sslipi=0.0d0 ssgradlipi=0.0 endif - print *, sslipi,ssgradlipi +! print *, sslipi,ssgradlipi dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) @@ -1385,16 +1640,37 @@ 'evdw',i,j,evdwij,' ss' ! if (energy_dec) write (iout,*) & ! 'evdw',i,j,evdwij,' ss' + do k=j+1,iend(i,iint) +!C search over all next residues + if (dyn_ss_mask(k)) then +!C check if they are cysteins +!C write(iout,*) 'k=',k + +!c write(iout,*) "PRZED TRI", evdwij +! evdwij_przed_tri=evdwij + call triple_ssbond_ene(i,j,k,evdwij) +!c if(evdwij_przed_tri.ne.evdwij) then +!c write (iout,*) "TRI:", evdwij, evdwij_przed_tri +!c endif + +!c write(iout,*) "PO TRI", evdwij +!C call the energy function that removes the artifical triple disulfide +!C bond the soubroutine is located in ssMD.F + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & + 'evdw',i,j,evdwij,'tss' + endif!dyn_ss_mask(k) + enddo! k ELSE !el ind=ind+1 - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle ! if (j.ne.78) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) ! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,& ! 1.0d0/vbld(j+nres) !d -! write (iout,*) "i",i," j", j," itype",itype(i),itype(j) +! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) chi2=chi(itypj,itypi) @@ -1516,7 +1792,7 @@ if (rij_shift.le.0.0D0) then evdw=1.0D20 !d write (iout,'(2(a3,i3,2x),17(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) return endif @@ -1539,7 +1815,7 @@ sigm=dabs(aa/bb)**(1.0D0/6.0D0) epsi=bb**2/aa!(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j, & + restyp(itypi,1),i,restyp(itypj,1),j, & epsi,sigm,chi1,chi2,chip1,chip2, & eps1,eps2rt**2,eps3rt**2,sig,sig0ij, & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift, & @@ -1551,6 +1827,7 @@ !C print *,i,j,c(1,i),c(1,j),c(2,i),c(2,j),c(3,i),c(3,j) ! if (energy_dec) write (iout,*) & ! 'evdw',i,j,evdwij +! print *,"ZALAMKA", evdw ! Calculate gradient components. e1=e1*eps1*eps2rt**2*eps3rt**2 @@ -1583,6 +1860,7 @@ enddo ! j enddo ! iint enddo ! i +! print *,"ZALAMKA", evdw ! write (iout,*) "Number of loop steps in EGB:",ind !ccc energy_dec=.false. return @@ -1621,9 +1899,9 @@ ! if (icall.eq.0) lprn=.true. !el ind=0 do i=iatsc_s,iatsc_e - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -1638,7 +1916,7 @@ do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -1700,7 +1978,7 @@ bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j,& + restyp(itypi,1),i,restyp(itypj,1),j,& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),& chi1,chi2,chip1,chip2,& eps1,eps2rt**2,eps3rt**2,& @@ -1753,9 +2031,9 @@ evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) if (itypi.eq.ntyp1) cycle - itypi1=iabs(itype(i+1)) + itypi1=iabs(itype(i+1,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -1766,7 +2044,7 @@ !d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint), !d & 'iend=',iend(i,iint) do j=istart(i,iint),iend(i,iint) - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -1840,7 +2118,7 @@ eello_turn4=0.0d0 !el ind=0 do i=iatel_s,iatel_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -1850,7 +2128,7 @@ num_conti=0 ! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) - if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle + if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle !el ind=ind+1 iteli=itel(i) itelj=itel(j) @@ -2101,8 +2379,8 @@ ! include 'COMMON.LOCAL' ! include 'COMMON.CHAIN' ! include 'COMMON.VECTORS' - real(kind=8),dimension(3,3,2,nres) :: uygradt,uzgradt !(3,3,2,maxres) - real(kind=8),dimension(3,nres) :: uyt,uzt !(3,maxres) + real(kind=8),dimension(3,3,2,nres) :: uygradt,uzgradt !(3,3,2,maxres) + real(kind=8),dimension(3,nres) :: uyt,uzt !(3,maxres) real(kind=8),dimension(3,3,2) :: uygradn,uzgradn real(kind=8),dimension(3) :: erij real(kind=8) :: delta=1.0d-7 @@ -2283,17 +2561,17 @@ endif ! if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then if (i.gt. nnt+2 .and. i.lt.nct+2) then - iti = itortyp(itype(i-2)) + iti = itortyp(itype(i-2,1)) else iti=ntortyp+1 endif ! if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - iti1 = itortyp(itype(i-1)) + iti1 = itortyp(itype(i-1,1)) else iti1=ntortyp+1 endif -! print *,iti,i,"iti",iti1,itype(i-1),itype(i-2) +! print *,iti,i,"iti",iti1,itype(i-1,1),itype(i-2,1) !d write (iout,*) '*******i',i,' iti1',iti !d write (iout,*) 'b1',b1(:,iti) !d write (iout,*) 'b2',b2(:,iti) @@ -2330,8 +2608,8 @@ enddo ! if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - if (itype(i-1).le.ntyp) then - iti1 = itortyp(itype(i-1)) + if (itype(i-1,1).le.ntyp) then + iti1 = itortyp(itype(i-1,1)) else iti1=ntortyp+1 endif @@ -2630,7 +2908,7 @@ #endif #endif !d do i=1,nres -!d iti = itortyp(itype(i)) +!d iti = itortyp(itype(i,1)) !d write (iout,*) i !d do j=1,2 !d write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)') @@ -2738,8 +3016,8 @@ ! write (iout,*) 'i',i,' fac',fac enddo endif - print *,wel_loc,"wel_loc",wcorr4,wcorr5,wcorr6,wturn3,wturn4, & - wturn6 +! print *,wel_loc,"wel_loc",wcorr4,wcorr5,wcorr6,wturn3,wturn4, & +! wturn6 if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or. & wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then @@ -2794,8 +3072,8 @@ ! print *,"before iturn3 loop" do i=iturn3_start,iturn3_end - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 & - .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 & + .or. itype(i+2,1).eq.ntyp1 .or. itype(i+3,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -2840,9 +3118,9 @@ num_cont_hb(i)=num_conti enddo do i=iturn4_start,iturn4_end - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 & - .or. itype(i+3).eq.ntyp1 & - .or. itype(i+4).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 & + .or. itype(i+3,1).eq.ntyp1 & + .or. itype(i+4,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -2883,15 +3161,16 @@ num_conti=num_cont_hb(i) call eelecij(i,i+3,ees,evdw1,eel_loc) - if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1) & + if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) & call eturn4(i,eello_turn4) num_cont_hb(i)=num_conti enddo ! i ! ! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 ! +! print *,"iatel_s,iatel_e,",iatel_s,iatel_e do i=iatel_s,iatel_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -2933,8 +3212,8 @@ ! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) num_conti=num_cont_hb(i) do j=ielstart(i),ielend(i) -! write (iout,*) i,j,itype(i),itype(j) - if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1) cycle +! write (iout,*) i,j,itype(i,1),itype(j,1) + if (itype(j,1).eq.ntyp1.or. itype(j+1,1).eq.ntyp1) cycle call eelecij(i,j,ees,evdw1,eel_loc) enddo ! j num_cont_hb(i)=num_conti @@ -3012,8 +3291,8 @@ ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,& ecosgp,ecosam,ecosbm,ecosgm,ghalf ! maxconts=nres/4 -! allocate(a_chuj(2,2,maxconts,nres)) !(2,2,maxconts,maxres) -! allocate(a_chuj_der(2,2,3,5,maxconts,nres)) !(2,2,3,5,maxconts,maxres) +! allocate(a_chuj(2,2,maxconts,nres)) !(2,2,maxconts,maxres) +! allocate(a_chuj_der(2,2,3,5,maxconts,nres)) !(2,2,3,5,maxconts,maxres) ! time00=MPI_Wtime() !d write (iout,*) "eelecij",i,j @@ -3436,7 +3715,7 @@ a32=a32*fac a33=a33*fac !d write (iout,'(4i5,4f10.5)') -!d & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33 +!d & i,itortyp(itype(i,1)),j,itortyp(itype(j,1)),a22,a23,a32,a33 !d write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij !d write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i), !d & uy(:,j),uz(:,j) @@ -4269,9 +4548,9 @@ a_temp(1,2)=a23 a_temp(2,1)=a32 a_temp(2,2)=a33 - iti1=itortyp(itype(i+1)) - iti2=itortyp(itype(i+2)) - iti3=itortyp(itype(i+3)) + iti1=itortyp(itype(i+1,1)) + iti2=itortyp(itype(i+2,1)) + iti3=itortyp(itype(i+3,1)) ! write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3 call transpose2(EUg(1,1,i+1),e1t(1,1)) call transpose2(Eug(1,1,i+2),e2t(1,1)) @@ -4494,7 +4773,7 @@ ! implicit none real(kind=8),dimension(3) :: u,vec real(kind=8),dimension(3,3) ::ugrad,ungrad - real(kind=8) :: unorm !,scalar + real(kind=8) :: unorm !,scalar integer :: i,j ! write (2,*) 'ugrad',ugrad ! write (2,*) 'u',u @@ -4540,7 +4819,7 @@ !d print '(a)','Enter ESCP' !d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e do i=iatscp_s,iatscp_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle iteli=itel(i) xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) @@ -4549,8 +4828,8 @@ do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - if (itype(j).eq.ntyp1) cycle - itypj=iabs(itype(j)) + if (itype(j,1).eq.ntyp1) cycle + itypj=iabs(itype(j,1)) ! Uncomment following three lines for SC-p interactions ! xj=c(1,nres+j)-xi ! yj=c(2,nres+j)-yi @@ -4644,7 +4923,7 @@ !d print '(a)','Enter ESCP' !d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e do i=iatscp_s,iatscp_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle iteli=itel(i) xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) @@ -4659,7 +4938,7 @@ do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) if (itypj.eq.ntyp1) cycle ! Uncomment following three lines for SC-p interactions ! xj=c(1,nres+j)-xi @@ -4835,51 +5114,107 @@ ! 18/07/06 MC: Use the convention that the first nss pairs are SS bonds if (.not.dyn_ss .and. i.le.nss) then ! 15/02/13 CC dynamic SSbond - additional check - if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and. & - iabs(itype(jjj)).eq.1) then + if (ii.gt.nres .and. iabs(itype(iii,1)).eq.1 .and. & + iabs(itype(jjj,1)).eq.1) then call ssbond_ene(iii,jjj,eij) ehpb=ehpb+2*eij !d write (iout,*) "eij",eij endif + else if (ii.gt.nres .and. jj.gt.nres) then +!c Restraints from contact prediction + dd=dist(ii,jj) + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)**4.0d0 & + *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 & + *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + if (energy_dec) write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, & + ehpb,fordepth(i),dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +!c write (iout,*) "beta nmr", +!c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + dd=dist(ii,jj) + rdis=dd-dhpb(i) +!C Get the force constant corresponding to this distance. + waga=forcon(i) +!C Calculate the contribution to energy. + ehpb=ehpb+waga*rdis*rdis +!c write (iout,*) "beta reg",dd,waga*rdis*rdis +!C +!C Evaluate gradient. +!C + fac=waga*rdis/dd + endif + endif + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo + do j=1,3 + ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) + ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) + enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo else -! Calculate the distance between the two points and its difference from the -! target distance. - dd=dist(ii,jj) - rdis=dd-dhpb(i) -! Get the force constant corresponding to this distance. - waga=forcon(i) -! Calculate the contribution to energy. - ehpb=ehpb+waga*rdis*rdis -! -! Evaluate gradient. -! - fac=waga*rdis/dd -!d print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd, -!d & ' waga=',waga,' fac=',fac - do j=1,3 - ggg(j)=fac*(c(j,jj)-c(j,ii)) - enddo -!d print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3) -! If this is a SC-SC distance, we need to calculate the contributions to the -! Cartesian gradient in the SC vectors (ghpbx). - if (iii.lt.ii) then + dd=dist(ii,jj) + if (constr_dist.eq.11) then + ehpb=ehpb+fordepth(i)**4.0d0 & + *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) + fac=fordepth(i)**4.0d0 & + *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd + if (energy_dec) write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj, & + ehpb,fordepth(i),dd + else + if (dhpb1(i).gt.0.0d0) then + ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd +!c write (iout,*) "alph nmr", +!c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) + else + rdis=dd-dhpb(i) +!C Get the force constant corresponding to this distance. + waga=forcon(i) +!C Calculate the contribution to energy. + ehpb=ehpb+waga*rdis*rdis +!c write (iout,*) "alpha reg",dd,waga*rdis*rdis +!C +!C Evaluate gradient. +!C + fac=waga*rdis/dd + endif + endif + + do j=1,3 + ggg(j)=fac*(c(j,jj)-c(j,ii)) + enddo +!cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3) +!C If this is a SC-SC distance, we need to calculate the contributions to the +!C Cartesian gradient in the SC vectors (ghpbx). + if (iii.lt.ii) then do j=1,3 ghpbx(j,iii)=ghpbx(j,iii)-ggg(j) ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j) enddo - endif -!grad do j=iii,jjj-1 -!grad do k=1,3 -!grad ghpbc(k,j)=ghpbc(k,j)+ggg(k) -!grad enddo -!grad enddo - do k=1,3 - ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) - ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) - enddo + endif +!cgrad do j=iii,jjj-1 +!cgrad do k=1,3 +!cgrad ghpbc(k,j)=ghpbc(k,j)+ggg(k) +!cgrad enddo +!cgrad enddo + do k=1,3 + ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k) + ghpbc(k,iii)=ghpbc(k,iii)-ggg(k) + enddo endif enddo - ehpb=0.5D0*ehpb + if (constr_dist.ne.11) ehpb=0.5D0*ehpb + return end subroutine edis !----------------------------------------------------------------------------- @@ -4908,7 +5243,7 @@ deltat1,deltat2,deltat12,ed,pom1,pom2,eom1,eom2,eom12,& cosphi,ggk - itypi=iabs(itype(i)) + itypi=iabs(itype(i,1)) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -4917,7 +5252,7 @@ dzi=dc_norm(3,nres+i) ! dsci_inv=dsc_inv(itypi) dsci_inv=vbld_inv(nres+i) - itypj=iabs(itype(j)) + itypj=iabs(itype(j,1)) ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(nres+j) xj=c(1,nres+j)-xi @@ -5007,8 +5342,8 @@ ! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres) do i=ibondp_start,ibondp_end - if (itype(i-1).eq.ntyp1 .and. itype(i).eq.ntyp1) cycle - if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then + if (itype(i-1,1).eq.ntyp1 .and. itype(i,1).eq.ntyp1) cycle + if (itype(i-1,1).eq.ntyp1 .or. itype(i,1).eq.ntyp1) then !C estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax) !C do j=1,3 !C gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax) & @@ -5030,11 +5365,13 @@ ! endif enddo estr=0.5d0*AKP*estr+estr1 +! print *,"estr_bb",estr,AKP ! ! 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included ! do i=ibond_start,ibond_end - iti=iabs(itype(i)) + iti=iabs(itype(i,1)) + if (iti.eq.0) print *,"WARNING WRONG SETTTING",i if (iti.ne.10 .and. iti.ne.ntyp1) then nbi=nbondterm(iti) if (nbi.eq.1) then @@ -5043,6 +5380,7 @@ "estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff,& AKSC(1,iti),AKSC(1,iti)*diff*diff estr=estr+0.5d0*AKSC(1,iti)*diff*diff +! print *,"estr_sc",estr do j=1,3 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) enddo @@ -5071,6 +5409,11 @@ usumsqder=usumsqder+ud(j)*uprod2 enddo estr=estr+uprod/usum +! print *,"estr_sc",estr,i + + if (energy_dec) write (iout,*) & + "estr sc",i,iti,vbld(i+nres),vbldsc0(1,iti),diff,& + AKSC(1,iti),uprod/usum do j=1,3 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres) enddo @@ -5120,24 +5463,24 @@ etheta=0.0D0 ! write (*,'(a,i2)') 'EBEND ICG=',icg do i=ithet_start,ithet_end - if (itype(i-1).eq.ntyp1) cycle + if (itype(i-1,1).eq.ntyp1) cycle ! Zero the energy function and its derivative at 0 or pi. call splinthet(theta(i),0.5d0*delta,ss,ssd) - it=itype(i-1) - ichir1=isign(1,itype(i-2)) - ichir2=isign(1,itype(i)) - if (itype(i-2).eq.10) ichir1=isign(1,itype(i-1)) - if (itype(i).eq.10) ichir2=isign(1,itype(i-1)) - if (itype(i-1).eq.10) then - itype1=isign(10,itype(i-2)) - ichir11=isign(1,itype(i-2)) - ichir12=isign(1,itype(i-2)) - itype2=isign(10,itype(i)) - ichir21=isign(1,itype(i)) - ichir22=isign(1,itype(i)) + it=itype(i-1,1) + ichir1=isign(1,itype(i-2,1)) + ichir2=isign(1,itype(i,1)) + if (itype(i-2,1).eq.10) ichir1=isign(1,itype(i-1,1)) + if (itype(i,1).eq.10) ichir2=isign(1,itype(i-1,1)) + if (itype(i-1,1).eq.10) then + itype1=isign(10,itype(i-2,1)) + ichir11=isign(1,itype(i-2,1)) + ichir12=isign(1,itype(i-2,1)) + itype2=isign(10,itype(i,1)) + ichir21=isign(1,itype(i,1)) + ichir22=isign(1,itype(i,1)) endif - if (i.gt.3 .and. itype(i-2).ne.ntyp1) then + if (i.gt.3 .and. itype(i-2,1).ne.ntyp1) then #ifdef OSF phii=phi(i) if (phii.ne.phii) phii=150.0 @@ -5150,7 +5493,7 @@ y(1)=0.0D0 y(2)=0.0D0 endif - if (i.lt.nres .and. itype(i).ne.ntyp1) then + if (i.lt.nres .and. itype(i,1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@ -5219,6 +5562,8 @@ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2 gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett) enddo +! print *,ithetaconstr_start,ithetaconstr_end,"TU" + ! Ufff.... We've done all this!!! return end subroutine ebend @@ -5314,7 +5659,7 @@ end subroutine theteng #else !----------------------------------------------------------------------------- - subroutine ebend(etheta) + subroutine ebend(etheta,ethetacnstr) ! ! Evaluate the virtual-bond-angle energy given the virtual-bond dihedral ! angles gamma and its derivatives in consecutive thetas and gammas. @@ -5340,31 +5685,34 @@ !el local variables integer :: i,k,iblock,ityp1,ityp2,ityp3,l,m real(kind=8) :: dethetai,dephii,dephii1,theti2,phii,phii1,ethetai - real(kind=8) :: aux,etheta,ccl,ssl,scl,csl + real(kind=8) :: aux,etheta,ccl,ssl,scl,csl,ethetacnstr +! local variables for constrains + real(kind=8) :: difi,thetiii + integer itheta etheta=0.0D0 do i=ithet_start,ithet_end - if (itype(i-1).eq.ntyp1) cycle - if (itype(i-2).eq.ntyp1.or.itype(i).eq.ntyp1) cycle - if (iabs(itype(i+1)).eq.20) iblock=2 - if (iabs(itype(i+1)).ne.20) iblock=1 + if (itype(i-1,1).eq.ntyp1) cycle + if (itype(i-2,1).eq.ntyp1.or.itype(i,1).eq.ntyp1) cycle + if (iabs(itype(i+1,1)).eq.20) iblock=2 + if (iabs(itype(i+1,1)).ne.20) iblock=1 dethetai=0.0d0 dephii=0.0d0 dephii1=0.0d0 theti2=0.5d0*theta(i) - ityp2=ithetyp((itype(i-1))) + ityp2=ithetyp((itype(i-1,1))) do k=1,nntheterm coskt(k)=dcos(k*theti2) sinkt(k)=dsin(k*theti2) enddo - if (i.gt.3 .and. itype(max0(i-3,1)).ne.ntyp1) then + if (i.gt.3 .and. itype(max0(i-3,1),1).ne.ntyp1) then #ifdef OSF phii=phi(i) if (phii.ne.phii) phii=150.0 #else phii=phi(i) #endif - ityp1=ithetyp((itype(i-2))) + ityp1=ithetyp((itype(i-2,1))) ! propagation of chirality for glycine type do k=1,nsingle cosph1(k)=dcos(k*phii) @@ -5372,13 +5720,13 @@ enddo else phii=0.0d0 - ityp1=ithetyp(itype(i-2)) + ityp1=ithetyp(itype(i-2,1)) do k=1,nsingle cosph1(k)=0.0d0 sinph1(k)=0.0d0 enddo endif - if (i.lt.nres .and. itype(i+1).ne.ntyp1) then + if (i.lt.nres .and. itype(i+1,1).ne.ntyp1) then #ifdef OSF phii1=phi(i+1) if (phii1.ne.phii1) phii1=150.0 @@ -5386,14 +5734,14 @@ #else phii1=phi(i+1) #endif - ityp3=ithetyp((itype(i))) + ityp3=ithetyp((itype(i,1))) do k=1,nsingle cosph2(k)=dcos(k*phii1) sinph2(k)=dsin(k*phii1) enddo else phii1=0.0d0 - ityp3=ithetyp(itype(i)) + ityp3=ithetyp(itype(i,1)) do k=1,nsingle cosph2(k)=0.0d0 sinph2(k)=0.0d0 @@ -5514,6 +5862,37 @@ if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1 gloc(nphi+i-2,icg)=wang*dethetai enddo +!-----------thete constrains +! if (tor_mode.ne.2) then + ethetacnstr=0.0d0 +! print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=ithetaconstr_start,ithetaconstr_end + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) & + +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) & + +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", & + i,itheta,rad2deg*thetiii, & + rad2deg*theta_constr0(i), rad2deg*theta_drange(i), & + rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, & + gloc(itheta+nphi-2,icg) + endif + enddo +! endif + return end subroutine ebend #endif @@ -5551,7 +5930,7 @@ escloc=0.0D0 ! write (iout,'(a)') 'ESC' do i=loc_start,loc_end - it=itype(i) + it=itype(i,1) if (it.eq.ntyp1) cycle if (it.eq.10) goto 1 nlobit=nlob(iabs(it)) @@ -5881,7 +6260,7 @@ delta=0.02d0*pi escloc=0.0D0 do i=loc_start,loc_end - if (itype(i).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1) cycle costtab(i+1) =dcos(theta(i+1)) sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1)) cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1))) @@ -5890,7 +6269,7 @@ cosfac=dsqrt(cosfac2) sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) - it=iabs(itype(i)) + it=iabs(itype(i,1)) if (it.eq.10) goto 1 ! ! Compute the axes of tghe local cartesian coordinates system; store in @@ -5908,7 +6287,7 @@ y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac enddo do j = 1,3 - z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i))) + z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i,1))) enddo ! write (2,*) "i",i ! write (2,*) "x_prime",(x_prime(j),j=1,3) @@ -5940,7 +6319,7 @@ ! Compute the energy of the ith side cbain ! ! write (2,*) "xx",xx," yy",yy," zz",zz - it=iabs(itype(i)) + it=iabs(itype(i,1)) do j = 1,65 x(j) = sc_parmin(j,it) enddo @@ -5948,7 +6327,7 @@ !c diagnostics - remove later xx1 = dcos(alph(2)) yy1 = dsin(alph(2))*dcos(omeg(2)) - zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2)) + zz1 = -dsign(1.0,dfloat(itype(i,1)))*dsin(alph(2))*dsin(omeg(2)) write(2,'(3f8.1,3f9.3,1x,3f9.3)') & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,& xx1,yy1,zz1 @@ -5990,7 +6369,7 @@ ! & dscp1,dscp2,sumene ! sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) escloc = escloc + sumene -! write (2,*) "i",i," escloc",sumene,escloc,it,itype(i) +! write (2,*) "i",i," escloc",sumene,escloc,it,itype(i,1) ! & ,zz,xx,yy !#define DEBUG #ifdef DEBUG @@ -6036,7 +6415,7 @@ ! ! Compute the gradient of esc ! -! zz=zz*dsign(1.0,dfloat(itype(i))) +! zz=zz*dsign(1.0,dfloat(itype(i,1))) pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2 pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2 pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2 @@ -6061,7 +6440,7 @@ +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6) & +(pom1+pom2)*pom_dx #ifdef DEBUG - write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i) + write(2,*), "de_dxx = ", de_dxx,de_dxx_num,itype(i,1) #endif ! sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz @@ -6076,7 +6455,7 @@ +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6) & +(pom1-pom2)*pom_dy #ifdef DEBUG - write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i) + write(2,*), "de_dyy = ", de_dyy,de_dyy_num,itype(i,1) #endif ! de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy & @@ -6088,14 +6467,14 @@ +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6) & + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6) #ifdef DEBUG - write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i) + write(2,*), "de_dzz = ", de_dzz,de_dzz_num,itype(i,1) #endif ! de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6) & -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6) & +pom1*pom_dt1+pom2*pom_dt2 #ifdef DEBUG - write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i) + write(2,*), "de_dt = ", de_dt,de_dt_num,itype(i,1) #endif ! ! @@ -6122,9 +6501,9 @@ dZZ_Ci(k)=0.0d0 do j=1,3 dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1) & - *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + *dsign(1.0d0,dfloat(itype(i,1)))*dC_norm(j,i+nres) dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1) & - *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres) + *dsign(1.0d0,dfloat(itype(i,1)))*dC_norm(j,i+nres) enddo dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres)) @@ -6324,10 +6703,10 @@ etors=0.0D0 do i=iphi_start,iphi_end etors_ii=0.0D0 - if (itype(i-2).eq.ntyp1.or. itype(i-1).eq.ntyp1 & - .or. itype(i).eq.ntyp1) cycle - itori=itortyp(itype(i-2)) - itori1=itortyp(itype(i-1)) + if (itype(i-2,1).eq.ntyp1.or. itype(i-1,1).eq.ntyp1 & + .or. itype(i,1).eq.ntyp1) cycle + itori=itortyp(itype(i-2,1)) + itori1=itortyp(itype(i-1,1)) phii=phi(i) gloci=0.0D0 ! Proline-Proline pair is a special case... @@ -6367,7 +6746,7 @@ 'etor',i,etors_ii if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & - restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,& + restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,itori,itori1,& (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci ! write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) @@ -6427,17 +6806,17 @@ ! lprn=.true. etors=0.0D0 do i=iphi_start,iphi_end - if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 & - .or. itype(i-3).eq.ntyp1 & - .or. itype(i).eq.ntyp1) cycle + if (itype(i-2,1).eq.ntyp1 .or. itype(i-1,1).eq.ntyp1 & + .or. itype(i-3,1).eq.ntyp1 & + .or. itype(i,1).eq.ntyp1) cycle etors_ii=0.0D0 - if (iabs(itype(i)).eq.20) then + if (iabs(itype(i,1)).eq.20) then iblock=2 else iblock=1 endif - itori=itortyp(itype(i-2)) - itori1=itortyp(itype(i-1)) + itori=itortyp(itype(i-2,1)) + itori1=itortyp(itype(i-1,1)) phii=phi(i) gloci=0.0D0 ! Regular cosine and sine terms @@ -6476,7 +6855,7 @@ 'etor',i,etors_ii-v0(itori,itori1,iblock) if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & - restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,& + restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,itori,itori1,& (v1(j,itori,itori1,iblock),j=1,6),& (v2(j,itori,itori1,iblock),j=1,6) gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci @@ -6538,18 +6917,18 @@ ! write(iout,*) "a tu??" do i=iphid_start,iphid_end etors_d_ii=0.0D0 - if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1 & - .or. itype(i-3).eq.ntyp1 & - .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle - itori=itortyp(itype(i-2)) - itori1=itortyp(itype(i-1)) - itori2=itortyp(itype(i)) + if (itype(i-2,1).eq.ntyp1 .or. itype(i-1,1).eq.ntyp1 & + .or. itype(i-3,1).eq.ntyp1 & + .or. itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle + itori=itortyp(itype(i-2,1)) + itori1=itortyp(itype(i-1,1)) + itori2=itortyp(itype(i,1)) phii=phi(i) phii1=phi(i+1) gloci1=0.0D0 gloci2=0.0D0 iblock=1 - if (iabs(itype(i+1)).eq.20) iblock=2 + if (iabs(itype(i+1,1)).eq.20) iblock=2 ! Regular cosine and sine terms do j=1,ntermd_1(itori,itori1,itori2,iblock) @@ -6629,10 +7008,10 @@ ! write (iout,*) "EBACK_SC_COR",itau_start,itau_end esccor=0.0D0 do i=itau_start,itau_end - if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle + if ((itype(i-2,1).eq.ntyp1).or.(itype(i-1,1).eq.ntyp1)) cycle esccor_ii=0.0D0 - isccori=isccortyp(itype(i-2)) - isccori1=isccortyp(itype(i-1)) + isccori=isccortyp(itype(i-2,1)) + isccori1=isccortyp(itype(i-1,1)) ! write (iout,*) "EBACK_SC_COR",i,nterm_sccor(isccori,isccori1) phii=phi(i) @@ -6644,17 +7023,17 @@ ! 2 = Ca...Ca...Ca...SC ! 3 = SC...Ca...Ca...SCi gloci=0.0D0 - if (((intertyp.eq.3).and.((itype(i-2).eq.10).or. & - (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or. & - (itype(i-1).eq.ntyp1))) & - .or. ((intertyp.eq.1).and.((itype(i-2).eq.10) & - .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1) & - .or.(itype(i).eq.ntyp1))) & - .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or. & - (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or. & - (itype(i-3).eq.ntyp1)))) cycle - if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle - if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1)) & + if (((intertyp.eq.3).and.((itype(i-2,1).eq.10).or. & + (itype(i-1,1).eq.10).or.(itype(i-2,1).eq.ntyp1).or. & + (itype(i-1,1).eq.ntyp1))) & + .or. ((intertyp.eq.1).and.((itype(i-2,1).eq.10) & + .or.(itype(i-2,1).eq.ntyp1).or.(itype(i-1,1).eq.ntyp1) & + .or.(itype(i,1).eq.ntyp1))) & + .or.((intertyp.eq.2).and.((itype(i-1,1).eq.10).or. & + (itype(i-1,1).eq.ntyp1).or.(itype(i-2,1).eq.ntyp1).or. & + (itype(i-3,1).eq.ntyp1)))) cycle + if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1,1).eq.ntyp1)) cycle + if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres,1).eq.ntyp1)) & cycle do j=1,nterm_sccor(isccori,isccori1) v1ij=v1sccor(j,intertyp,isccori,isccori1) @@ -6671,7 +7050,7 @@ gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci if (lprn) & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & - restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1,& + restyp(itype(i-2,1),1),i-2,restyp(itype(i-1,1),1),i-1,isccori,isccori1,& (v1sccor(j,intertyp,isccori,isccori1),j=1,6),& (v2sccor(j,intertyp,isccori,isccori1),j=1,6) gsccor_loc(i-3)=gsccor_loc(i-3)+gloci @@ -7791,9 +8170,9 @@ allocate(dipderx(3,5,4,maxconts,nres)) ! - iti1 = itortyp(itype(i+1)) + iti1 = itortyp(itype(i+1,1)) if (j.lt.nres-1) then - itj1 = itortyp(itype(j+1)) + itj1 = itortyp(itype(j+1,1)) else itj1=ntortyp+1 endif @@ -7886,14 +8265,14 @@ if (l.eq.j+1) then ! parallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itortyp(itype(i,1)) else iti=ntortyp+1 endif - itk1=itortyp(itype(k+1)) - itj=itortyp(itype(j)) + itk1=itortyp(itype(k+1,1)) + itj=itortyp(itype(j,1)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itortyp(itype(l+1,1)) else itl1=ntortyp+1 endif @@ -8039,15 +8418,15 @@ else ! Antiparallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itortyp(itype(i,1)) else iti=ntortyp+1 endif - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk1=itortyp(itype(k+1,1)) + itl=itortyp(itype(l,1)) + itj=itortyp(itype(j,1)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itortyp(itype(j+1,1)) else itj1=ntortyp+1 endif @@ -8364,7 +8743,7 @@ ! o o o o C ! /l\ / \ \ / \ / \ / C ! / \ / \ \ / \ / \ / C -! j| o |l1 | o | o| o | | o |o C +! j| o |l1 | o | o| o | | o |o C ! \ |/k\| |/ \| / |/ \| |/ \| C ! \i/ \ / \ / / \ / \ C ! o k1 o C @@ -8377,7 +8756,7 @@ ! o o o o C ! /j\ / \ \ / \ / \ / C ! / \ / \ \ / \ / \ / C -! j1| o |l | o | o| o | | o |o C +! j1| o |l | o | o| o | | o |o C ! \ |/k\| |/ \| / |/ \| |/ \| C ! \i/ \ / \ / / \ / \ C ! o k1 o C @@ -8395,9 +8774,9 @@ !d write (iout,*) !d & 'EELLO5: Contacts have occurred for peptide groups',i,j, !d & ' and',k,l - itk=itortyp(itype(k)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk=itortyp(itype(k,1)) + itl=itortyp(itype(l,1)) + itj=itortyp(itype(j,1)) eello5_1=0.0d0 eello5_2=0.0d0 eello5_3=0.0d0 @@ -8925,7 +9304,7 @@ ! i i C ! C !CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - itk=itortyp(itype(k)) + itk=itortyp(itype(k,1)) s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i)) s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k)) s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k)) @@ -9221,16 +9600,16 @@ ! ! 4/7/01 AL Component s1 was removed, because it pertains to the respective ! energy moment and not to the cluster cumulant. - iti=itortyp(itype(i)) + iti=itortyp(itype(i,1)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itortyp(itype(j+1,1)) else itj1=ntortyp+1 endif - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) + itk=itortyp(itype(k,1)) + itk1=itortyp(itype(k+1,1)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itortyp(itype(l+1,1)) else itl1=ntortyp+1 endif @@ -9342,22 +9721,22 @@ ! 4/7/01 AL Component s1 was removed, because it pertains to the respective ! energy moment and not to the cluster cumulant. !d write (2,*) 'eello_graph4: wturn6',wturn6 - iti=itortyp(itype(i)) - itj=itortyp(itype(j)) + iti=itortyp(itype(i,1)) + itj=itortyp(itype(j,1)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itortyp(itype(j+1,1)) else itj1=ntortyp+1 endif - itk=itortyp(itype(k)) + itk=itortyp(itype(k,1)) if (k.lt.nres-1) then - itk1=itortyp(itype(k+1)) + itk1=itortyp(itype(k+1,1)) else itk1=ntortyp+1 endif - itl=itortyp(itype(l)) + itl=itortyp(itype(l,1)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itortyp(itype(l+1,1)) else itl1=ntortyp+1 endif @@ -9584,11 +9963,11 @@ j=i+4 k=i+1 l=i+3 - iti=itortyp(itype(i)) - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + iti=itortyp(itype(i,1)) + itk=itortyp(itype(k,1)) + itk1=itortyp(itype(k+1,1)) + itl=itortyp(itype(l,1)) + itj=itortyp(itype(j,1)) !d write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj !d write (2,*) 'i',i,' k',k,' j',j,' l',l !d if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then @@ -10127,11 +10506,27 @@ wturn6*gcorr6_turn_long(j,i)+ & wstrain*ghpbc(j,i) & +wliptran*gliptranc(j,i) & + +gradafm(j,i) & +welec*gshieldc(j,i) & +wcorr*gshieldc_ec(j,i) & +wturn3*gshieldc_t3(j,i)& +wturn4*gshieldc_t4(j,i)& - +wel_loc*gshieldc_ll(j,i) + +wel_loc*gshieldc_ll(j,i)& + +wtube*gg_tube(j,i) & + +wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)+ & + wvdwpsb*(gvdwpsb(j,i)+gvdwpsb1(j,i))+ & + wvdwsb*gvdwsbc(j,i)+welsb*gelsbc(j,i)+ & + wcorr_nucl*gradcorr_nucl(j,i)& + +wcorr3_nucl*gradcorr3_nucl(j,i)+& + wcatprot* gradpepcat(j,i)+ & + wcatcat*gradcatcat(j,i)+ & + wscbase*gvdwc_scbase(j,i)+ & + wpepbase*gvdwc_pepbase(j,i)+& + wscpho*gvdwc_scpho(j,i)+ & + wpeppho*gvdwc_peppho(j,i) + + + enddo @@ -10150,10 +10545,23 @@ wturn6*gcorr6_turn_long(j,i)+ & wstrain*ghpbc(j,i) & +wliptran*gliptranc(j,i) & + +gradafm(j,i) & +welec*gshieldc(j,i)& +wcorr*gshieldc_ec(j,i) & +wturn4*gshieldc_t4(j,i) & - +wel_loc*gshieldc_ll(j,i) + +wel_loc*gshieldc_ll(j,i)& + +wtube*gg_tube(j,i) & + +wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)+ & + wvdwpsb*(gvdwpsb(j,i)+gvdwpsb1(j,i))+ & + wvdwsb*gvdwsbc(j,i)+welsb*gelsbc(j,i)+ & + wcorr_nucl*gradcorr_nucl(j,i) & + +wcorr3_nucl*gradcorr3_nucl(j,i) +& + wcatprot* gradpepcat(j,i)+ & + wcatcat*gradcatcat(j,i)+ & + wscbase*gvdwc_scbase(j,i) & + wpepbase*gvdwc_pepbase(j,i)+& + wscpho*gvdwc_scpho(j,i)+& + wpeppho*gvdwc_peppho(j,i) enddo @@ -10300,6 +10708,7 @@ wsccor*gsccorc(j,i) & +wscloc*gscloc(j,i) & +wliptran*gliptranc(j,i) & + +gradafm(j,i) & +welec*gshieldc(j,i) & +welec*gshieldc_loc(j,i) & +wcorr*gshieldc_ec(j,i) & @@ -10309,7 +10718,50 @@ +wturn4*gshieldc_t4(j,i) & +wturn4*gshieldc_loc_t4(j,i) & +wel_loc*gshieldc_ll(j,i) & - +wel_loc*gshieldc_loc_ll(j,i) + +wel_loc*gshieldc_loc_ll(j,i) & + +wtube*gg_tube(j,i) & + +0.5d0*(wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)& + +wvdwpsb*gvdwpsb1(j,i))& + +wbond_nucl*gradb_nucl(j,i)+wsbloc*gsbloc(j,i) + +! if ((i.le.2).and.(i.ge.1)) +! print *,gradc(j,i,icg),& +! gradbufc(j,i),welec*gelc(j,i), & +! wel_loc*gel_loc(j,i), & +! wscp*gvdwc_scpp(j,i), & +! welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i), & +! wel_loc*gel_loc_long(j,i), & +! wcorr*gradcorr_long(j,i), & +! wcorr5*gradcorr5_long(j,i), & +! wcorr6*gradcorr6_long(j,i), & +! wturn6*gcorr6_turn_long(j,i), & +! wbond*gradb(j,i), & +! wcorr*gradcorr(j,i), & +! wturn3*gcorr3_turn(j,i), & +! wturn4*gcorr4_turn(j,i), & +! wcorr5*gradcorr5(j,i), & +! wcorr6*gradcorr6(j,i), & +! wturn6*gcorr6_turn(j,i), & +! wsccor*gsccorc(j,i) & +! ,wscloc*gscloc(j,i) & +! ,wliptran*gliptranc(j,i) & +! ,gradafm(j,i) & +! ,welec*gshieldc(j,i) & +! ,welec*gshieldc_loc(j,i) & +! ,wcorr*gshieldc_ec(j,i) & +! ,wcorr*gshieldc_loc_ec(j,i) & +! ,wturn3*gshieldc_t3(j,i) & +! ,wturn3*gshieldc_loc_t3(j,i) & +! ,wturn4*gshieldc_t4(j,i) & +! ,wturn4*gshieldc_loc_t4(j,i) & +! ,wel_loc*gshieldc_ll(j,i) & +! ,wel_loc*gshieldc_loc_ll(j,i) & +! ,wtube*gg_tube(j,i) & +! ,wbond_nucl*gradb_nucl(j,i) & +! ,wvdwpp_nucl*gvdwpp_nucl(j,i),welpp*gelpp(j,i),& +! wvdwpsb*gvdwpsb1(j,i)& +! ,wbond_nucl*gradb_nucl(j,i),wsbloc*gsbloc(j,i) +! #else gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ & @@ -10330,6 +10782,7 @@ wturn6*gcorr6_turn(j,i)+ & wsccor*gsccorc(j,i) & +wscloc*gscloc(j,i) & + +gradafm(j,i) & +wliptran*gliptranc(j,i) & +welec*gshieldc(j,i) & +welec*gshieldc_loc(j,) & @@ -10340,7 +10793,14 @@ +wturn4*gshieldc_t4(j,i) & +wturn4*gshieldc_loc_t4(j,i) & +wel_loc*gshieldc_ll(j,i) & - +wel_loc*gshieldc_loc_ll(j,i) + +wel_loc*gshieldc_loc_ll(j,i) & + +wtube*gg_tube(j,i) & + +wbond_nucl*gradb_nucl(j,i) & + +0.5d0*(wvdwpp_nucl*gvdwpp_nucl(j,i)+welpp*gelpp(j,i)& + +wvdwpsb*gvdwpsb1(j,i))& + +wsbloc*gsbloc(j,i) + + #endif @@ -10354,7 +10814,19 @@ +wcorr*gshieldx_ec(j,i) & +wturn3*gshieldx_t3(j,i) & +wturn4*gshieldx_t4(j,i) & - +wel_loc*gshieldx_ll(j,i) + +wel_loc*gshieldx_ll(j,i)& + +wtube*gg_tube_sc(j,i) & + +wbond_nucl*gradbx_nucl(j,i) & + +wvdwsb*gvdwsbx(j,i) & + +welsb*gelsbx(j,i) & + +wcorr_nucl*gradxorr_nucl(j,i)& + +wcorr3_nucl*gradxorr3_nucl(j,i) & + +wsbloc*gsblocx(j,i) & + +wcatprot* gradpepcatx(j,i)& + +wscbase*gvdwx_scbase(j,i) & + +wpepbase*gvdwx_pepbase(j,i)& + +wscpho*gvdwx_scpho(j,i) +! if (i.eq.3) print *,"tu?", wscpho,gvdwx_scpho(j,i) enddo enddo @@ -10382,7 +10854,7 @@ #ifdef MPI if (nfgtasks.gt.1) then do j=1,3 - do i=1,nres + do i=0,nres gradbufc(j,i)=gradc(j,i,icg) gradbufx(j,i)=gradx(j,i,icg) enddo @@ -10411,7 +10883,7 @@ time00=MPI_Wtime() call MPI_Reduce(gradbufc(1,0),gradc(1,0,icg),3*nres+3,& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) - call MPI_Reduce(gradbufx(1,1),gradx(1,1,icg),3*nres,& + call MPI_Reduce(gradbufx(1,0),gradx(1,0,icg),3*nres+3,& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) call MPI_Reduce(glocbuf(1),gloc(1,icg),4*nres,& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) @@ -10420,6 +10892,7 @@ MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR) time_reduce=time_reduce+MPI_Wtime()-time00 !#define DEBUG +! print *,"gradbuf",gradbufc(1,1),gradc(1,1,icg) #ifdef DEBUG write (iout,*) "gloc_sc after reduce" do i=1,nres @@ -10563,7 +11036,7 @@ ! include 'COMMON.CALC' ! include 'COMMON.IOUNITS' real(kind=8), dimension(3) :: dcosom1,dcosom2 - +! print *,"wchodze" eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 & @@ -10794,7 +11267,7 @@ ! ind1=0 do i=1,nres-2 - ind1=ind1+1 + ind1=ind1+1 ! ! Derivatives of DC(i+1) in theta(i+2) ! @@ -10883,8 +11356,8 @@ ! theta(nres) and phi(i+3) thru phi(nres). ! do j=i+1,nres-2 - ind1=ind1+1 - ind=indmat(i+1,j+1) + ind1=ind1+1 + ind=indmat(i+1,j+1) !d print *,'i=',i,' j=',j,' ind=',ind,' ind1=',ind1 do k=1,3 do l=1,3 @@ -10925,7 +11398,7 @@ enddo do k=1,3 dcdv(k+3,ind1)=vbld(i+1)*temp(k,1) - enddo + enddo do k=1,3 dxoijk=0.0D0 do l=1,3 @@ -10939,7 +11412,7 @@ ! Derivatives in alpha and omega: ! do i=2,nres-1 -! dsci=dsc(itype(i)) +! dsci=dsc(itype(i,1)) dsci=vbld(i+nres) #ifdef OSF alphi=alph(i) @@ -10947,43 +11420,43 @@ if(alphi.ne.alphi) alphi=100.0 if(omegi.ne.omegi) omegi=-100.0 #else - alphi=alph(i) - omegi=omeg(i) + alphi=alph(i) + omegi=omeg(i) #endif !d print *,'i=',i,' dsci=',dsci,' alphi=',alphi,' omegi=',omegi - cosalphi=dcos(alphi) - sinalphi=dsin(alphi) - cosomegi=dcos(omegi) - sinomegi=dsin(omegi) - temp(1,1)=-dsci*sinalphi - temp(2,1)= dsci*cosalphi*cosomegi - temp(3,1)=-dsci*cosalphi*sinomegi - temp(1,2)=0.0D0 - temp(2,2)=-dsci*sinalphi*sinomegi - temp(3,2)=-dsci*sinalphi*cosomegi - theta2=pi-0.5D0*theta(i+1) - cost2=dcos(theta2) - sint2=dsin(theta2) - jjj=0 + cosalphi=dcos(alphi) + sinalphi=dsin(alphi) + cosomegi=dcos(omegi) + sinomegi=dsin(omegi) + temp(1,1)=-dsci*sinalphi + temp(2,1)= dsci*cosalphi*cosomegi + temp(3,1)=-dsci*cosalphi*sinomegi + temp(1,2)=0.0D0 + temp(2,2)=-dsci*sinalphi*sinomegi + temp(3,2)=-dsci*sinalphi*cosomegi + theta2=pi-0.5D0*theta(i+1) + cost2=dcos(theta2) + sint2=dsin(theta2) + jjj=0 !d print *,((temp(l,k),l=1,3),k=1,2) do j=1,2 - xp=temp(1,j) - yp=temp(2,j) - xxp= xp*cost2+yp*sint2 - yyp=-xp*sint2+yp*cost2 - zzp=temp(3,j) - xx(1)=xxp - xx(2)=yyp*r(2,2,i-1)+zzp*r(2,3,i-1) - xx(3)=yyp*r(3,2,i-1)+zzp*r(3,3,i-1) - do k=1,3 - dj=0.0D0 - do l=1,3 - dj=dj+prod(k,l,i-1)*xx(l) + xp=temp(1,j) + yp=temp(2,j) + xxp= xp*cost2+yp*sint2 + yyp=-xp*sint2+yp*cost2 + zzp=temp(3,j) + xx(1)=xxp + xx(2)=yyp*r(2,2,i-1)+zzp*r(2,3,i-1) + xx(3)=yyp*r(3,2,i-1)+zzp*r(3,3,i-1) + do k=1,3 + dj=0.0D0 + do l=1,3 + dj=dj+prod(k,l,i-1)*xx(l) enddo - dxds(jjj+k,i)=dj + dxds(jjj+k,i)=dj enddo - jjj=jjj+3 - enddo + jjj=jjj+3 + enddo enddo return end subroutine cartder @@ -11015,33 +11488,33 @@ write (iout,'(a)') '**************** dx/dalpha' write (iout,'(a)') do i=2,nres-1 - alphi=alph(i) - alph(i)=alph(i)+aincr - do k=1,3 - temp(k,i)=dc(k,nres+i) + alphi=alph(i) + alph(i)=alph(i)+aincr + do k=1,3 + temp(k,i)=dc(k,nres+i) enddo - call chainbuild - do k=1,3 - gg(k)=(dc(k,nres+i)-temp(k,i))/aincr - xx(k)=dabs((gg(k)-dxds(k,i))/(aincr*dabs(dxds(k,i))+aincr)) + call chainbuild + do k=1,3 + gg(k)=(dc(k,nres+i)-temp(k,i))/aincr + xx(k)=dabs((gg(k)-dxds(k,i))/(aincr*dabs(dxds(k,i))+aincr)) enddo write (iout,'(i4,3e15.6/4x,3e15.6,3f9.3)') & i,(gg(k),k=1,3),(dxds(k,i),k=1,3),(xx(k),k=1,3) write (iout,'(a)') - alph(i)=alphi - call chainbuild + alph(i)=alphi + call chainbuild enddo write (iout,'(a)') write (iout,'(a)') '**************** dx/domega' write (iout,'(a)') do i=2,nres-1 - omegi=omeg(i) - omeg(i)=omeg(i)+aincr - do k=1,3 - temp(k,i)=dc(k,nres+i) + omegi=omeg(i) + omeg(i)=omeg(i)+aincr + do k=1,3 + temp(k,i)=dc(k,nres+i) enddo - call chainbuild - do k=1,3 + call chainbuild + do k=1,3 gg(k)=(dc(k,nres+i)-temp(k,i))/aincr xx(k)=dabs((gg(k)-dxds(k+3,i))/ & (aincr*dabs(dxds(k+3,i))+aincr)) @@ -11049,14 +11522,14 @@ write (iout,'(i4,3e15.6/4x,3e15.6,3f9.3)') & i,(gg(k),k=1,3),(dxds(k+3,i),k=1,3),(xx(k),k=1,3) write (iout,'(a)') - omeg(i)=omegi - call chainbuild + omeg(i)=omegi + call chainbuild enddo write (iout,'(a)') write (iout,'(a)') '**************** dx/dtheta' write (iout,'(a)') do i=3,nres - theti=theta(i) + theti=theta(i) theta(i)=theta(i)+aincr do j=i-1,nres-1 do k=1,3 @@ -11065,11 +11538,11 @@ enddo call chainbuild do j=i-1,nres-1 - ii = indmat(i-2,j) + ii = indmat(i-2,j) ! print *,'i=',i-2,' j=',j-1,' ii=',ii - do k=1,3 - gg(k)=(dc(k,nres+j)-temp(k,j))/aincr - xx(k)=dabs((gg(k)-dxdv(k,ii))/ & + do k=1,3 + gg(k)=(dc(k,nres+j)-temp(k,j))/aincr + xx(k)=dabs((gg(k)-dxdv(k,ii))/ & (aincr*dabs(dxdv(k,ii))+aincr)) enddo write (iout,'(2i4,3e14.6/8x,3e14.6,3f9.3)') & @@ -11091,10 +11564,10 @@ enddo call chainbuild do j=i-1,nres-1 - ii = indmat(i-2,j) + ii = indmat(i-2,j) ! print *,'ii=',ii - do k=1,3 - gg(k)=(dc(k,nres+j)-temp(k,j))/aincr + do k=1,3 + gg(k)=(dc(k,nres+j)-temp(k,j))/aincr xx(k)=dabs((gg(k)-dxdv(k+3,ii))/ & (aincr*dabs(dxdv(k+3,ii))+aincr)) enddo @@ -11116,16 +11589,16 @@ enddo call chainbuild do j=i+1,nres-1 - ii = indmat(i,j) + ii = indmat(i,j) ! print *,'ii=',ii - do k=1,3 - gg(k)=(dc(k,j)-temp(k,j))/aincr - xx(k)=dabs((gg(k)-dcdv(k,ii))/ & + do k=1,3 + gg(k)=(dc(k,j)-temp(k,j))/aincr + xx(k)=dabs((gg(k)-dcdv(k,ii))/ & (aincr*dabs(dcdv(k,ii))+aincr)) enddo write (iout,'(2i4,3e14.6/8x,3e14.6,3f9.3)') & i,j,(gg(k),k=1,3),(dcdv(k,ii),k=1,3),(xx(k),k=1,3) - write (iout,'(a)') + write (iout,'(a)') enddo do j=1,nres do k=1,3 @@ -11145,16 +11618,16 @@ enddo call chainbuild do j=i+2,nres-1 - ii = indmat(i+1,j) + ii = indmat(i+1,j) ! print *,'ii=',ii - do k=1,3 - gg(k)=(dc(k,j)-temp(k,j))/aincr + do k=1,3 + gg(k)=(dc(k,j)-temp(k,j))/aincr xx(k)=dabs((gg(k)-dcdv(k+3,ii))/ & (aincr*dabs(dcdv(k+3,ii))+aincr)) enddo write (iout,'(2i4,3e14.6/8x,3e14.6,3f9.3)') & i,j,(gg(k),k=1,3),(dcdv(k+3,ii),k=1,3),(xx(k),k=1,3) - write (iout,'(a)') + write (iout,'(a)') enddo do j=1,nres do k=1,3 @@ -11206,44 +11679,44 @@ write (iout,'(i5,3f10.5)') i,(gradxorr(j,i),j=1,3) enddo do i=1,nres - do j=1,3 - grad_s(j,i)=gradc(j,i,icg) - grad_s(j+3,i)=gradx(j,i,icg) + do j=1,3 + grad_s(j,i)=gradc(j,i,icg) + grad_s(j+3,i)=gradx(j,i,icg) enddo enddo call flush(iout) write (iout,'(/a/)') 'Gradient in virtual-bond and SC vectors' do i=1,nres do j=1,3 - xx(j)=c(j,i+nres) - ddc(j)=dc(j,i) - ddx(j)=dc(j,i+nres) - enddo - do j=1,3 - dc(j,i)=dc(j,i)+aincr - do k=i+1,nres - c(j,k)=c(j,k)+aincr - c(j,k+nres)=c(j,k+nres)+aincr + xx(j)=c(j,i+nres) + ddc(j)=dc(j,i) + ddx(j)=dc(j,i+nres) + enddo + do j=1,3 + dc(j,i)=dc(j,i)+aincr + do k=i+1,nres + c(j,k)=c(j,k)+aincr + c(j,k+nres)=c(j,k+nres)+aincr enddo call etotal(energia1) etot1=energia1(0) - ggg(j)=(etot1-etot)/aincr - dc(j,i)=ddc(j) - do k=i+1,nres - c(j,k)=c(j,k)-aincr - c(j,k+nres)=c(j,k+nres)-aincr + ggg(j)=(etot1-etot)/aincr + dc(j,i)=ddc(j) + do k=i+1,nres + c(j,k)=c(j,k)-aincr + c(j,k+nres)=c(j,k+nres)-aincr enddo enddo - do j=1,3 - c(j,i+nres)=c(j,i+nres)+aincr - dc(j,i+nres)=dc(j,i+nres)+aincr + do j=1,3 + c(j,i+nres)=c(j,i+nres)+aincr + dc(j,i+nres)=dc(j,i+nres)+aincr call etotal(energia1) etot1=energia1(0) - ggg(j+3)=(etot1-etot)/aincr - c(j,i+nres)=xx(j) - dc(j,i+nres)=ddx(j) + ggg(j+3)=(etot1-etot)/aincr + c(j,i+nres)=xx(j) + dc(j,i+nres)=ddx(j) enddo - write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/)') & + write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/)') & i,(ggg(k),k=1,6),(grad_s(k,i),k=1,6) enddo return @@ -11357,7 +11830,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo call zerograd call etotal_short(energia) -!el call enerprint(energia) + call enerprint(energia) call flush(iout) write (iout,*) "enter cartgrad" call flush(iout) @@ -11386,14 +11859,14 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do j=1,3 if (nnt.gt.1 .and. i.eq.nnt) ddc1(j)=c(j,1) if (nct.lt.nres .and. i.eq.nct) ddcn(j)=c(j,nres) - ddc(j)=c(j,i) - ddx(j)=c(j,i+nres) + ddc(j)=c(j,i) + ddx(j)=c(j,i+nres) dcnorm_safe1(j)=dc_norm(j,i-1) dcnorm_safe2(j)=dc_norm(j,i) dxnorm_safe(j)=dc_norm(j,i+nres) enddo - do j=1,3 - c(j,i)=ddc(j)+aincr + do j=1,3 + c(j,i)=ddc(j)+aincr if (nnt.gt.1 .and. i.eq.nnt) c(j,1)=c(j,1)+aincr if (nct.lt.nres .and. i.eq.nct) c(j,nres)=c(j,nres)+aincr if (i.gt.1) dc(j,i-1)=c(j,i)-c(j,i-1) @@ -11413,7 +11886,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' endif !- end split gradient ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1 - c(j,i)=ddc(j)-aincr + c(j,i)=ddc(j)-aincr if (nnt.gt.1 .and. i.eq.nnt) c(j,1)=ddc1(j)-aincr if (nct.lt.nres .and. i.eq.nct) c(j,nres)=ddcn(j)-aincr if (i.gt.1) dc(j,i-1)=c(j,i)-c(j,i-1) @@ -11424,20 +11897,20 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' call etotal(energia1) etot2=energia1(0) write (iout,*) "ij",i,j," etot2",etot2 - ggg(j)=(etot1-etot2)/(2*aincr) + ggg(j)=(etot1-etot2)/(2*aincr) else !- split gradient call etotal_long(energia1) etot21=energia1(0) - ggg(j)=(etot11-etot21)/(2*aincr) + ggg(j)=(etot11-etot21)/(2*aincr) call etotal_short(energia1) etot22=energia1(0) - ggg1(j)=(etot12-etot22)/(2*aincr) + ggg1(j)=(etot12-etot22)/(2*aincr) !- end split gradient ! write (iout,*) "etot21",etot21," etot22",etot22 endif ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot2",etot2 - c(j,i)=ddc(j) + c(j,i)=ddc(j) if (nnt.gt.1 .and. i.eq.nnt) c(j,1)=ddc1(j) if (nct.lt.nres .and. i.eq.nct) c(j,nres)=ddcn(j) if (i.gt.1) dc(j,i-1)=c(j,i)-c(j,i-1) @@ -11447,8 +11920,8 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' dc_norm(j,i)=dcnorm_safe2(j) dc_norm(j,i+nres)=dxnorm_safe(j) enddo - do j=1,3 - c(j,i+nres)=ddx(j)+aincr + do j=1,3 + c(j,i+nres)=ddx(j)+aincr dc(j,i+nres)=c(j,i+nres)-c(j,i) call int_from_cart1(.false.) if (.not.split_ene) then @@ -11462,30 +11935,30 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' etot12=energia1(0) endif !- end split gradient - c(j,i+nres)=ddx(j)-aincr + c(j,i+nres)=ddx(j)-aincr dc(j,i+nres)=c(j,i+nres)-c(j,i) call int_from_cart1(.false.) if (.not.split_ene) then call etotal(energia1) etot2=energia1(0) - ggg(j+3)=(etot1-etot2)/(2*aincr) + ggg(j+3)=(etot1-etot2)/(2*aincr) else !- split gradient call etotal_long(energia1) etot21=energia1(0) - ggg(j+3)=(etot11-etot21)/(2*aincr) + ggg(j+3)=(etot11-etot21)/(2*aincr) call etotal_short(energia1) etot22=energia1(0) - ggg1(j+3)=(etot12-etot22)/(2*aincr) + ggg1(j+3)=(etot12-etot22)/(2*aincr) !- end split gradient endif ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot2",etot2 - c(j,i+nres)=ddx(j) + c(j,i+nres)=ddx(j) dc(j,i+nres)=c(j,i+nres)-c(j,i) dc_norm(j,i+nres)=dxnorm_safe(j) call int_from_cart1(.false.) enddo - write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & + write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & i,(ggg(k),k=1,6),(grad_s(k,i),k=1,6),(ggg(k)/grad_s(k,i),k=1,6) if (split_ene) then write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & @@ -11564,6 +12037,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do i=1,nres do j=1,3 grad_s(j,i)=gcart(j,i) +! if (i.le.2) print *,"tu?!",gcart(j,i),grad_s(j,i),gxcart(j,i) grad_s(j+3,i)=gxcart(j,i) enddo enddo @@ -11621,16 +12095,16 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' write (iout,'(/a/)') 'Gradient in virtual-bond and SC vectors' do i=0,nres do j=1,3 - xx(j)=c(j,i+nres) - ddc(j)=dc(j,i) - ddx(j)=dc(j,i+nres) + xx(j)=c(j,i+nres) + ddc(j)=dc(j,i) + ddx(j)=dc(j,i+nres) do k=1,3 dcnorm_safe(k)=dc_norm(k,i) dxnorm_safe(k)=dc_norm(k,i+nres) enddo enddo - do j=1,3 - dc(j,i)=ddc(j)+aincr + do j=1,3 + dc(j,i)=ddc(j)+aincr call chainbuild_cart #ifdef MPI ! Broadcast the order to compute internal coordinates to the slaves. @@ -11641,6 +12115,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if (.not.split_ene) then call etotal(energia1) etot1=energia1(0) +! call enerprint(energia1) else !- split gradient call etotal_long(energia1) @@ -11651,30 +12126,30 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' endif !- end split gradient ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1 - dc(j,i)=ddc(j)-aincr + dc(j,i)=ddc(j)-aincr call chainbuild_cart ! call int_from_cart1(.false.) if (.not.split_ene) then call etotal(energia1) etot2=energia1(0) - ggg(j)=(etot1-etot2)/(2*aincr) + ggg(j)=(etot1-etot2)/(2*aincr) else !- split gradient call etotal_long(energia1) etot21=energia1(0) - ggg(j)=(etot11-etot21)/(2*aincr) + ggg(j)=(etot11-etot21)/(2*aincr) call etotal_short(energia1) etot22=energia1(0) - ggg1(j)=(etot12-etot22)/(2*aincr) + ggg1(j)=(etot12-etot22)/(2*aincr) !- end split gradient ! write (iout,*) "etot21",etot21," etot22",etot22 endif ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot2",etot2 - dc(j,i)=ddc(j) + dc(j,i)=ddc(j) call chainbuild_cart enddo - do j=1,3 - dc(j,i+nres)=ddx(j)+aincr + do j=1,3 + dc(j,i+nres)=ddx(j)+aincr call chainbuild_cart ! write (iout,*) "i",i," j",j," dxnorm+ and dxnorm" ! write (iout,'(3f15.10)') (dc_norm(k,i+nres),k=1,3) @@ -11696,7 +12171,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' endif !- end split gradient ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot1",etot1 - dc(j,i+nres)=ddx(j)-aincr + dc(j,i+nres)=ddx(j)-aincr call chainbuild_cart ! write (iout,*) "i",i," j",j," dxnorm- and dxnorm" ! write (iout,'(3f15.10)') (dc_norm(k,i+nres),k=1,3) @@ -11709,22 +12184,22 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if (.not.split_ene) then call etotal(energia1) etot2=energia1(0) - ggg(j+3)=(etot1-etot2)/(2*aincr) + ggg(j+3)=(etot1-etot2)/(2*aincr) else !- split gradient call etotal_long(energia1) etot21=energia1(0) - ggg(j+3)=(etot11-etot21)/(2*aincr) + ggg(j+3)=(etot11-etot21)/(2*aincr) call etotal_short(energia1) etot22=energia1(0) - ggg1(j+3)=(etot12-etot22)/(2*aincr) + ggg1(j+3)=(etot12-etot22)/(2*aincr) !- end split gradient endif ! write(iout,'(2i5,2(a,f15.10))')i,j," etot",etot," etot2",etot2 - dc(j,i+nres)=ddx(j) + dc(j,i+nres)=ddx(j) call chainbuild_cart enddo - write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & + write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & i,(ggg(k),k=1,6),(grad_s(k,i),k=1,6),(ggg(k)/grad_s(k,i),k=1,6) if (split_ene) then write (iout,'(i3,6(1pe12.5)/3x,6(1pe12.5)/3x,6(1pe12.5)/)') & @@ -11769,11 +12244,11 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' call var_to_geom(nvar,x) call chainbuild icall=1 - print *,'ICG=',ICG +! print *,'ICG=',ICG call etotal(energia) etot = energia(0) !el call enerprint(energia) - print *,'ICG=',ICG +! print *,'ICG=',ICG #ifdef MPL if (MyID.ne.BossID) then call mp_bcast(x(1),8*(nvar+3),BossID,fgGroupID) @@ -12027,9 +12502,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12040,7 +12515,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint), !d & 'iend=',iend(i,iint) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -12117,9 +12592,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12132,7 +12607,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint), !d & 'iend=',iend(i,iint) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -12207,9 +12682,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12218,7 +12693,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -12238,7 +12713,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) !d epsi=bb(itypi,itypj)**2/aa(itypi,itypj) !d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)') -!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), +!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj), !d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, !d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, !d & (c(k,i),k=1,3),(c(k,j),k=1,3) @@ -12294,9 +12769,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12305,7 +12780,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle xj=c(1,nres+j)-xi yj=c(2,nres+j)-yi @@ -12325,7 +12800,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) !d epsi=bb(itypi,itypj)**2/aa(itypi,itypj) !d write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)') -!d & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj), +!d & restyp(itypi,1),i,restyp(itypj,1),j,aa(itypi,itypj), !d & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm, !d & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij, !d & (c(k,i),k=1,3),(c(k,j),k=1,3) @@ -12393,9 +12868,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! endif !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12410,7 +12885,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -12451,7 +12926,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) !d write (iout,'(2(a3,i3,2x),15(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & epsi,sigm,chi1,chi2,chip1,chip2, !d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq), !d & om1,om2,om12,1.0D0/dsqrt(rrij), @@ -12513,9 +12988,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! endif !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12530,7 +13005,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -12571,7 +13046,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) !d write (iout,'(2(a3,i3,2x),15(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & epsi,sigm,chi1,chi2,chip1,chip2, !d & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq), !d & om1,om2,om12,1.0D0/dsqrt(rrij), @@ -12633,9 +13108,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! if (icall.eq.0) lprn=.false. !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12681,21 +13156,43 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN - call dyn_ssbond_ene(i,j,evdwij) - evdw=evdw+evdwij - if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & - 'evdw',i,j,evdwij,' ss' +! call dyn_ssbond_ene(i,j,evdwij) +! evdw=evdw+evdwij +! if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & +! 'evdw',i,j,evdwij,' ss' ! if (energy_dec) write (iout,*) & ! 'evdw',i,j,evdwij,' ss' +! do k=j+1,iend(i,iint) +!C search over all next residues +! if (dyn_ss_mask(k)) then +!C check if they are cysteins +!C write(iout,*) 'k=',k + +!c write(iout,*) "PRZED TRI", evdwij +! evdwij_przed_tri=evdwij +! call triple_ssbond_ene(i,j,k,evdwij) +!c if(evdwij_przed_tri.ne.evdwij) then +!c write (iout,*) "TRI:", evdwij, evdwij_przed_tri +!c endif + +!c write(iout,*) "PO TRI", evdwij +!C call the energy function that removes the artifical triple disulfide +!C bond the soubroutine is located in ssMD.F +! evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & + 'evdw',i,j,evdwij,'tss' +! endif!dyn_ss_mask(k) +! enddo! k + ELSE !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) ! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv, ! & 1.0d0/vbld(j+nres) -! write (iout,*) "i",i," j", j," itype",itype(i),itype(j) +! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) chi2=chi(itypj,itypi) @@ -12799,7 +13296,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if (rij_shift.le.0.0D0) then evdw=1.0D20 !d write (iout,'(2(a3,i3,2x),17(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) return endif @@ -12820,7 +13317,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j,& + restyp(itypi,1),i,restyp(itypj,1),j,& epsi,sigm,chi1,chi2,chip1,chip2,& eps1,eps2rt**2,eps3rt**2,sig,sig0ij,& om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,& @@ -12891,9 +13388,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! if (icall.eq.0) lprn=.false. !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -12949,17 +13446,39 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' evdw=evdw+evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' + do k=j+1,iend(i,iint) +!C search over all next residues + if (dyn_ss_mask(k)) then +!C check if they are cysteins +!C write(iout,*) 'k=',k + +!c write(iout,*) "PRZED TRI", evdwij +! evdwij_przed_tri=evdwij + call triple_ssbond_ene(i,j,k,evdwij) +!c if(evdwij_przed_tri.ne.evdwij) then +!c write (iout,*) "TRI:", evdwij, evdwij_przed_tri +!c endif + +!c write(iout,*) "PO TRI", evdwij +!C call the energy function that removes the artifical triple disulfide +!C bond the soubroutine is located in ssMD.F + evdw=evdw+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & + 'evdw',i,j,evdwij,'tss' + endif!dyn_ss_mask(k) + enddo! k + ! if (energy_dec) write (iout,*) & ! 'evdw',i,j,evdwij,' ss' ELSE !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) ! write (iout,*) "j",j,dsc_inv(itypj),dscj_inv, ! & 1.0d0/vbld(j+nres) -! write (iout,*) "i",i," j", j," itype",itype(i),itype(j) +! write (iout,*) "i",i," j", j," itype",itype(i,1),itype(j,1) sig0ij=sigma(itypi,itypj) chi1=chi(itypi,itypj) chi2=chi(itypj,itypi) @@ -13068,7 +13587,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if (rij_shift.le.0.0D0) then evdw=1.0D20 !d write (iout,'(2(a3,i3,2x),17(0pf7.3))') -!d & restyp(itypi),i,restyp(itypj),j, +!d & restyp(itypi,1),i,restyp(itypj,1),j, !d & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq) return endif @@ -13089,7 +13608,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j,& + restyp(itypi,1),i,restyp(itypj,1),j,& epsi,sigm,chi1,chi2,chip1,chip2,& eps1,eps2rt**2,eps3rt**2,sig,sig0ij,& om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,& @@ -13159,9 +13678,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! if (icall.eq.0) lprn=.true. !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -13176,7 +13695,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -13232,7 +13751,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j,& + restyp(itypi,1),i,restyp(itypj,1),j,& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),& chi1,chi2,chip1,chip2,& eps1,eps2rt**2,eps3rt**2,& @@ -13288,9 +13807,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! if (icall.eq.0) lprn=.true. !el ind=0 do i=iatsc_s,iatsc_e - itypi=itype(i) + itypi=itype(i,1) if (itypi.eq.ntyp1) cycle - itypi1=itype(i+1) + itypi1=itype(i+1,1) xi=c(1,nres+i) yi=c(2,nres+i) zi=c(3,nres+i) @@ -13305,7 +13824,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nint_gr(i) do j=istart(i,iint),iend(i,iint) !el ind=ind+1 - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) @@ -13361,7 +13880,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sigm=dabs(aa_aq(itypi,itypj)/bb_aq(itypi,itypj))**(1.0D0/6.0D0) epsi=bb_aq(itypi,itypj)**2/aa_aq(itypi,itypj) write (iout,'(2(a3,i3,2x),17(0pf7.3))') & - restyp(itypi),i,restyp(itypj),j,& + restyp(itypi,1),i,restyp(itypj,1),j,& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),& chi1,chi2,chip1,chip2,& eps1,eps2rt**2,eps3rt**2,& @@ -13512,8 +14031,8 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! Loop over i,i+2 and i,i+3 pairs of the peptide groups ! do i=iturn3_start,iturn3_end - if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1 & - .or. itype(i+2).eq.ntyp1 .or. itype(i+3).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1.or. itype(i+1,1).eq.ntyp1 & + .or. itype(i+2,1).eq.ntyp1 .or. itype(i+3,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -13535,9 +14054,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' num_cont_hb(i)=num_conti enddo do i=iturn4_start,iturn4_end - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 & - .or. itype(i+3).eq.ntyp1 & - .or. itype(i+4).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1 & + .or. itype(i+3,1).eq.ntyp1 & + .or. itype(i+4,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -13555,7 +14074,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if (zmedi.lt.0) zmedi=zmedi+boxzsize num_conti=num_cont_hb(i) call eelecij_scale(i,i+3,ees,evdw1,eel_loc) - if (wturn4.gt.0.0d0 .and. itype(i+2).ne.ntyp1) & + if (wturn4.gt.0.0d0 .and. itype(i+2,1).ne.ntyp1) & call eturn4(i,eello_turn4) num_cont_hb(i)=num_conti enddo ! i @@ -13563,7 +14082,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 ! do i=iatel_s,iatel_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -13582,7 +14101,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) num_conti=num_cont_hb(i) do j=ielstart(i),ielend(i) - if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle + if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle call eelecij_scale(i,j,ees,evdw1,eel_loc) enddo ! j num_cont_hb(i)=num_conti @@ -13674,8 +14193,8 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! allocate(d_cont(maxconts,nres)) !(maxconts,maxres) ! allocate(jcont_hb(maxconts,nres)) !(maxconts,maxres) -! allocate(a_chuj(2,2,maxconts,nres)) !(2,2,maxconts,maxres) -! allocate(a_chuj_der(2,2,3,5,maxconts,nres)) !(2,2,3,5,maxconts,maxres) +! allocate(a_chuj(2,2,maxconts,nres)) !(2,2,maxconts,maxres) +! allocate(a_chuj_der(2,2,3,5,maxconts,nres)) !(2,2,3,5,maxconts,maxres) #ifdef MPI time00=MPI_Wtime() @@ -13966,7 +14485,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' a32=a32*fac a33=a33*fac !d write (iout,'(4i5,4f10.5)') -!d & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33 +!d & i,itortyp(itype(i,1)),j,itortyp(itype(j,1)),a22,a23,a32,a33 !d write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij !d write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') uy(:,i),uz(:,i), !d & uy(:,j),uz(:,j) @@ -14443,7 +14962,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! & " iatel_e_vdw",iatel_e_vdw call flush(iout) do i=iatel_s_vdw,iatel_e_vdw - if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1.or. itype(i+1,1).eq.ntyp1) cycle dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -14464,7 +14983,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! & ' ielend',ielend_vdw(i) call flush(iout) do j=ielstart_vdw(i),ielend_vdw(i) - if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1) cycle + if (itype(j,1).eq.ntyp1 .or. itype(j+1,1).eq.ntyp1) cycle !el ind=ind+1 iteli=itel(i) itelj=itel(j) @@ -14597,7 +15116,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d print '(a)','Enter ESCP' !d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e do i=iatscp_s,iatscp_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle iteli=itel(i) xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) @@ -14612,7 +15131,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! Uncomment following three lines for SC-p interactions ! xj=c(1,nres+j)-xi @@ -14756,7 +15275,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !d print '(a)','Enter ESCP' !d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e do i=iatscp_s,iatscp_e - if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1 .or. itype(i+1,1).eq.ntyp1) cycle iteli=itel(i) xi=0.5D0*(c(1,i)+c(1,i+1)) yi=0.5D0*(c(2,i)+c(2,i+1)) @@ -14771,7 +15290,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do iint=1,nscp_gr(i) do j=iscpstart(i,iint),iscpend(i,iint) - itypj=itype(j) + itypj=itype(j,1) if (itypj.eq.ntyp1) cycle ! Uncomment following three lines for SC-p interactions ! xj=c(1,nres+j)-xi @@ -15231,7 +15750,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !el local variables integer :: i,nres6 real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,esccor,etors_d,etors - real(kind=8) :: ehpb,escloc,estr,ebe,edihcnstr + real(kind=8) :: ehpb,escloc,estr,ebe,edihcnstr,ethetacnstr nres6=6*nres ! write(iout,'(a,i2)')'Calling etotal_short ipot=',ipot @@ -15386,7 +15905,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! ! Calculate the virtual-bond-angle energy. ! - call ebend(ebe) + call ebend(ebe,ethetacnstr) ! ! Calculate the SC local energy. ! @@ -15472,7 +15991,35 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' endif return end function gnmr1prim -!----------------------------------------------------------------------------- +!---------------------------------------------------------------------------- + real(kind=8) function rlornmr1(y,ymin,ymax,sigma) + real(kind=8) y,ymin,ymax,sigma + real(kind=8) wykl /4.0d0/ + if (y.lt.ymin) then + rlornmr1=(ymin-y)**wykl/((ymin-y)**wykl+sigma**wykl) + else if (y.gt.ymax) then + rlornmr1=(y-ymax)**wykl/((y-ymax)**wykl+sigma**wykl) + else + rlornmr1=0.0d0 + endif + return + end function rlornmr1 +!------------------------------------------------------------------------------ + real(kind=8) function rlornmr1prim(y,ymin,ymax,sigma) + real(kind=8) y,ymin,ymax,sigma + real(kind=8) wykl /4.0d0/ + if (y.lt.ymin) then + rlornmr1prim=-(ymin-y)**(wykl-1)*sigma**wykl*wykl/ & + ((ymin-y)**wykl+sigma**wykl)**2 + else if (y.gt.ymax) then + rlornmr1prim=(y-ymax)**(wykl-1)*sigma**wykl*wykl/ & + ((y-ymax)**wykl+sigma**wykl)**2 + else + rlornmr1prim=0.0d0 + endif + return + end function rlornmr1prim + real(kind=8) function harmonic(y,ymax) ! implicit none real(kind=8) :: y,ymax @@ -15540,44 +16087,44 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ind=0 ind1=0 do i=1,nres-2 - gthetai=0.0D0 - gphii=0.0D0 - do j=i+1,nres-1 + gthetai=0.0D0 + gphii=0.0D0 + do j=i+1,nres-1 ind=ind+1 ! ind=indmat(i,j) ! print *,'GRAD: i=',i,' jc=',j,' ind=',ind - do k=1,3 + do k=1,3 gthetai=gthetai+dcdv(k,ind)*gradc(k,j,icg) enddo - do k=1,3 - gphii=gphii+dcdv(k+3,ind)*gradc(k,j,icg) + do k=1,3 + gphii=gphii+dcdv(k+3,ind)*gradc(k,j,icg) enddo enddo - do j=i+1,nres-1 + do j=i+1,nres-1 ind1=ind1+1 ! ind1=indmat(i,j) ! print *,'GRAD: i=',i,' jx=',j,' ind1=',ind1 - do k=1,3 - gthetai=gthetai+dxdv(k,ind1)*gradx(k,j,icg) - gphii=gphii+dxdv(k+3,ind1)*gradx(k,j,icg) + do k=1,3 + gthetai=gthetai+dxdv(k,ind1)*gradx(k,j,icg) + gphii=gphii+dxdv(k+3,ind1)*gradx(k,j,icg) enddo enddo - if (i.gt.1) g(i-1)=gphii - if (n.gt.nphi) g(nphi+i)=gthetai + if (i.gt.1) g(i-1)=gphii + if (n.gt.nphi) g(nphi+i)=gthetai enddo if (n.le.nphi+ntheta) goto 10 do i=2,nres-1 - if (itype(i).ne.10) then + if (itype(i,1).ne.10) then galphai=0.0D0 - gomegai=0.0D0 - do k=1,3 - galphai=galphai+dxds(k,i)*gradx(k,i,icg) + gomegai=0.0D0 + do k=1,3 + galphai=galphai+dxds(k,i)*gradx(k,i,icg) enddo - do k=1,3 - gomegai=gomegai+dxds(k+3,i)*gradx(k,i,icg) + do k=1,3 + gomegai=gomegai+dxds(k+3,i)*gradx(k,i,icg) enddo g(ialph(i,1))=galphai - g(ialph(i,1)+nside)=gomegai + g(ialph(i,1)+nside)=gomegai endif enddo ! @@ -15612,7 +16159,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' real(kind=8) :: urparm(1) real(kind=8) :: f real(kind=8),external :: ufparm - real(kind=8),dimension(6*nres) :: x !(maxvar) (maxvar=6*maxres) + real(kind=8),dimension(6*nres) :: x !(maxvar) (maxvar=6*maxres) ! if (jjj.gt.0) then ! write (iout,'(10f8.3)') (rad2deg*x(i),i=1,n) ! endif @@ -15705,6 +16252,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do j=1,3 gcart(j,i)=gradc(j,i,icg) gxcart(j,i)=gradx(j,i,icg) +! if (i.le.2) print *,"gcart_one",gcart(j,i),gradc(j,i,icg) enddo #ifdef DEBUG write (iout,'(i5,2(3f10.5,5x),f10.5)') i,(gcart(j,i),j=1,3),& @@ -15714,817 +16262,853 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' #ifdef TIMING time01=MPI_Wtime() #endif +! print *,"gcart_two",gxcart(2,2),gradx(2,2,icg) call int_to_cart +! print *,"gcart_two",gxcart(2,2),gradx(2,2,icg) + #ifdef TIMING - time_inttocart=time_inttocart+MPI_Wtime()-time01 + time_inttocart=time_inttocart+MPI_Wtime()-time01 #endif #ifdef DEBUG - write (iout,*) "gcart and gxcart after int_to_cart" - do i=0,nres-1 - write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),& - (gxcart(j,i),j=1,3) - enddo + write (iout,*) "gcart and gxcart after int_to_cart" + do i=0,nres-1 + write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),& + (gxcart(j,i),j=1,3) + enddo #endif #ifdef CARGRAD #ifdef DEBUG - write (iout,*) "CARGRAD" + write (iout,*) "CARGRAD" #endif - do i=nres,0,-1 - do j=1,3 - gcart(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i) -! gcart_new(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i) - enddo -! write (iout,'(i5,3f10.5,5x,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3), & -! (gcart_new(j,i),j=1,3),(gxcart(j,i),j=1,3) - enddo -! Correction: dummy residues - if (nnt.gt.1) then - do j=1,3 -! gcart_new(j,nnt)=gcart_new(j,nnt)+gcart_new(j,1) - gcart(j,nnt)=gcart(j,nnt)+gcart(j,1) - enddo - endif - if (nct.lt.nres) then - do j=1,3 -! gcart_new(j,nct)=gcart_new(j,nct)+gcart_new(j,nres) - gcart(j,nct)=gcart(j,nct)+gcart(j,nres) - enddo - endif + do i=nres,0,-1 + do j=1,3 + gcart(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i) + ! gcart_new(j,i)=-gcart(j,i)+gcart(j,i-1)-gxcart(j,i) + enddo + ! write (iout,'(i5,3f10.5,5x,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3), & + ! (gcart_new(j,i),j=1,3),(gxcart(j,i),j=1,3) + enddo + ! Correction: dummy residues + if (nnt.gt.1) then + do j=1,3 + ! gcart_new(j,nnt)=gcart_new(j,nnt)+gcart_new(j,1) + gcart(j,nnt)=gcart(j,nnt)+gcart(j,1) + enddo + endif + if (nct.lt.nres) then + do j=1,3 + ! gcart_new(j,nct)=gcart_new(j,nct)+gcart_new(j,nres) + gcart(j,nct)=gcart(j,nct)+gcart(j,nres) + enddo + endif #endif #ifdef TIMING - time_cartgrad=time_cartgrad+MPI_Wtime()-time00 + time_cartgrad=time_cartgrad+MPI_Wtime()-time00 #endif -!el#undef DEBUG - return - end subroutine cartgrad -!----------------------------------------------------------------------------- - subroutine zerograd -! implicit real*8 (a-h,o-z) -! include 'DIMENSIONS' -! include 'COMMON.DERIV' -! include 'COMMON.CHAIN' -! include 'COMMON.VAR' -! include 'COMMON.MD' -! include 'COMMON.SCCOR' -! -!el local variables - integer :: i,j,intertyp,k -! Initialize Cartesian-coordinate gradient -! -! if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2) -! if (.not.allocated(gradc)) allocate(gradc(3,nres,2)) !(3,maxres,2) - -! allocate(gvdwx(3,nres),gvdwc(3,nres),gelc(3,nres),gelc_long(3,nres)) -! allocate(gvdwpp(3,nres),gvdwc_scpp(3,nres),gradx_scp(3,nres)) -! allocate(gvdwc_scp(3,nres),ghpbx(3,nres),ghpbc(3,nres)) -! allocate(gradcorr_long(3,nres)) -! allocate(gradcorr5_long(3,nres),gradcorr6_long(3,nres)) -! allocate(gcorr6_turn_long(3,nres)) -! allocate(gradcorr5(3,nres),gradcorr6(3,nres)) !(3,maxres) - -! if (.not.allocated(gradcorr)) allocate(gradcorr(3,nres)) !(3,maxres) - -! allocate(gel_loc(3,nres),gel_loc_long(3,nres),gcorr3_turn(3,nres)) -! allocate(gcorr4_turn(3,nres),gcorr6_turn(3,nres)) - -! if (.not.allocated(gradb)) allocate(gradb(3,nres)) !(3,maxres) -! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres) - -! allocate(gsccorc(3,nres),gsccorx(3,nres)) !(3,maxres) -! allocate(gscloc(3,nres)) !(3,maxres) -! if (.not.allocated(gsclocx)) allocate(gsclocx(3,nres)) !(3,maxres) - - - -! common /deriv_scloc/ -! allocate(dXX_C1tab(3,nres),dYY_C1tab(3,nres),dZZ_C1tab(3,nres)) -! allocate(dXX_Ctab(3,nres),dYY_Ctab(3,nres),dZZ_Ctab(3,nres)) -! allocate(dXX_XYZtab(3,nres),dYY_XYZtab(3,nres),dZZ_XYZtab(3,nres)) !(3,maxres) -! common /mpgrad/ -! allocate(jgrad_start(nres),jgrad_end(nres)) !(maxres) - - - -! gradc(j,i,icg)=0.0d0 -! gradx(j,i,icg)=0.0d0 - -! allocate(gloc_sc(3,nres,10)) !(3,0:maxres2,10)maxres2=2*maxres -!elwrite(iout,*) "icg",icg - do i=-1,nres - do j=1,3 - gvdwx(j,i)=0.0D0 - gradx_scp(j,i)=0.0D0 - gvdwc(j,i)=0.0D0 - gvdwc_scp(j,i)=0.0D0 - gvdwc_scpp(j,i)=0.0d0 - gelc(j,i)=0.0D0 - gelc_long(j,i)=0.0D0 - gradb(j,i)=0.0d0 - gradbx(j,i)=0.0d0 - gvdwpp(j,i)=0.0d0 - gel_loc(j,i)=0.0d0 - gel_loc_long(j,i)=0.0d0 - ghpbc(j,i)=0.0D0 - ghpbx(j,i)=0.0D0 - gcorr3_turn(j,i)=0.0d0 - gcorr4_turn(j,i)=0.0d0 - gradcorr(j,i)=0.0d0 - gradcorr_long(j,i)=0.0d0 - gradcorr5_long(j,i)=0.0d0 - gradcorr6_long(j,i)=0.0d0 - gcorr6_turn_long(j,i)=0.0d0 - gradcorr5(j,i)=0.0d0 - gradcorr6(j,i)=0.0d0 - gcorr6_turn(j,i)=0.0d0 - gsccorc(j,i)=0.0d0 - gsccorx(j,i)=0.0d0 - gradc(j,i,icg)=0.0d0 - gradx(j,i,icg)=0.0d0 - gscloc(j,i)=0.0d0 - gsclocx(j,i)=0.0d0 - gliptran(j,i)=0.0d0 - gliptranx(j,i)=0.0d0 - gliptranc(j,i)=0.0d0 - gshieldx(j,i)=0.0d0 - gshieldc(j,i)=0.0d0 - gshieldc_loc(j,i)=0.0d0 - gshieldx_ec(j,i)=0.0d0 - gshieldc_ec(j,i)=0.0d0 - gshieldc_loc_ec(j,i)=0.0d0 - gshieldx_t3(j,i)=0.0d0 - gshieldc_t3(j,i)=0.0d0 - gshieldc_loc_t3(j,i)=0.0d0 - gshieldx_t4(j,i)=0.0d0 - gshieldc_t4(j,i)=0.0d0 - gshieldc_loc_t4(j,i)=0.0d0 - gshieldx_ll(j,i)=0.0d0 - gshieldc_ll(j,i)=0.0d0 - gshieldc_loc_ll(j,i)=0.0d0 - - do intertyp=1,3 - gloc_sc(intertyp,i,icg)=0.0d0 - enddo - enddo - enddo - do i=1,nres - do j=1,maxcontsshi - shield_list(j,i)=0 - do k=1,3 -!C print *,i,j,k - grad_shield_side(k,j,i)=0.0d0 - grad_shield_loc(k,j,i)=0.0d0 - enddo - enddo - ishield_list(i)=0 - enddo - -! -! Initialize the gradient of local energy terms. -! -! allocate(gloc(4*nres,2)) !!(maxvar,2)(maxvar=6*maxres) -! if (.not.allocated(gel_loc_loc)) allocate(gel_loc_loc(nres)) !(maxvar)(maxvar=6*maxres) -! if (.not.allocated(gcorr_loc)) allocate(gcorr_loc(nres)) !(maxvar)(maxvar=6*maxres) -! allocate(g_corr5_loc(nres),g_corr6_loc(nres)) !(maxvar)(maxvar=6*maxres) -! allocate(gel_loc_turn3(nres)) -! allocate(gel_loc_turn4(nres),gel_loc_turn6(nres)) !(maxvar)(maxvar=6*maxres) -! allocate(gsccor_loc(nres)) !(maxres) + !el#undef DEBUG + return + end subroutine cartgrad + !----------------------------------------------------------------------------- + subroutine zerograd + ! implicit real*8 (a-h,o-z) + ! include 'DIMENSIONS' + ! include 'COMMON.DERIV' + ! include 'COMMON.CHAIN' + ! include 'COMMON.VAR' + ! include 'COMMON.MD' + ! include 'COMMON.SCCOR' + ! + !el local variables + integer :: i,j,intertyp,k + ! Initialize Cartesian-coordinate gradient + ! + ! if (.not.allocated(gradx)) allocate(gradx(3,nres,2)) !(3,maxres,2) + ! if (.not.allocated(gradc)) allocate(gradc(3,nres,2)) !(3,maxres,2) + + ! allocate(gvdwx(3,nres),gvdwc(3,nres),gelc(3,nres),gelc_long(3,nres)) + ! allocate(gvdwpp(3,nres),gvdwc_scpp(3,nres),gradx_scp(3,nres)) + ! allocate(gvdwc_scp(3,nres),ghpbx(3,nres),ghpbc(3,nres)) + ! allocate(gradcorr_long(3,nres)) + ! allocate(gradcorr5_long(3,nres),gradcorr6_long(3,nres)) + ! allocate(gcorr6_turn_long(3,nres)) + ! allocate(gradcorr5(3,nres),gradcorr6(3,nres)) !(3,maxres) + + ! if (.not.allocated(gradcorr)) allocate(gradcorr(3,nres)) !(3,maxres) + + ! allocate(gel_loc(3,nres),gel_loc_long(3,nres),gcorr3_turn(3,nres)) + ! allocate(gcorr4_turn(3,nres),gcorr6_turn(3,nres)) + + ! if (.not.allocated(gradb)) allocate(gradb(3,nres)) !(3,maxres) + ! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres) + + ! allocate(gsccorc(3,nres),gsccorx(3,nres)) !(3,maxres) + ! allocate(gscloc(3,nres)) !(3,maxres) + ! if (.not.allocated(gsclocx)) allocate(gsclocx(3,nres)) !(3,maxres) + + + + ! common /deriv_scloc/ + ! allocate(dXX_C1tab(3,nres),dYY_C1tab(3,nres),dZZ_C1tab(3,nres)) + ! allocate(dXX_Ctab(3,nres),dYY_Ctab(3,nres),dZZ_Ctab(3,nres)) + ! allocate(dXX_XYZtab(3,nres),dYY_XYZtab(3,nres),dZZ_XYZtab(3,nres)) !(3,maxres) + ! common /mpgrad/ + ! allocate(jgrad_start(nres),jgrad_end(nres)) !(maxres) + + + + ! gradc(j,i,icg)=0.0d0 + ! gradx(j,i,icg)=0.0d0 + + ! allocate(gloc_sc(3,nres,10)) !(3,0:maxres2,10)maxres2=2*maxres + !elwrite(iout,*) "icg",icg + do i=-1,nres + do j=1,3 + gvdwx(j,i)=0.0D0 + gradx_scp(j,i)=0.0D0 + gvdwc(j,i)=0.0D0 + gvdwc_scp(j,i)=0.0D0 + gvdwc_scpp(j,i)=0.0d0 + gelc(j,i)=0.0D0 + gelc_long(j,i)=0.0D0 + gradb(j,i)=0.0d0 + gradbx(j,i)=0.0d0 + gvdwpp(j,i)=0.0d0 + gel_loc(j,i)=0.0d0 + gel_loc_long(j,i)=0.0d0 + ghpbc(j,i)=0.0D0 + ghpbx(j,i)=0.0D0 + gcorr3_turn(j,i)=0.0d0 + gcorr4_turn(j,i)=0.0d0 + gradcorr(j,i)=0.0d0 + gradcorr_long(j,i)=0.0d0 + gradcorr5_long(j,i)=0.0d0 + gradcorr6_long(j,i)=0.0d0 + gcorr6_turn_long(j,i)=0.0d0 + gradcorr5(j,i)=0.0d0 + gradcorr6(j,i)=0.0d0 + gcorr6_turn(j,i)=0.0d0 + gsccorc(j,i)=0.0d0 + gsccorx(j,i)=0.0d0 + gradc(j,i,icg)=0.0d0 + gradx(j,i,icg)=0.0d0 + gscloc(j,i)=0.0d0 + gsclocx(j,i)=0.0d0 + gliptran(j,i)=0.0d0 + gliptranx(j,i)=0.0d0 + gliptranc(j,i)=0.0d0 + gshieldx(j,i)=0.0d0 + gshieldc(j,i)=0.0d0 + gshieldc_loc(j,i)=0.0d0 + gshieldx_ec(j,i)=0.0d0 + gshieldc_ec(j,i)=0.0d0 + gshieldc_loc_ec(j,i)=0.0d0 + gshieldx_t3(j,i)=0.0d0 + gshieldc_t3(j,i)=0.0d0 + gshieldc_loc_t3(j,i)=0.0d0 + gshieldx_t4(j,i)=0.0d0 + gshieldc_t4(j,i)=0.0d0 + gshieldc_loc_t4(j,i)=0.0d0 + gshieldx_ll(j,i)=0.0d0 + gshieldc_ll(j,i)=0.0d0 + gshieldc_loc_ll(j,i)=0.0d0 + gg_tube(j,i)=0.0d0 + gg_tube_sc(j,i)=0.0d0 + gradafm(j,i)=0.0d0 + gradb_nucl(j,i)=0.0d0 + gradbx_nucl(j,i)=0.0d0 + gvdwpp_nucl(j,i)=0.0d0 + gvdwpp(j,i)=0.0d0 + gelpp(j,i)=0.0d0 + gvdwpsb(j,i)=0.0d0 + gvdwpsb1(j,i)=0.0d0 + gvdwsbc(j,i)=0.0d0 + gvdwsbx(j,i)=0.0d0 + gelsbc(j,i)=0.0d0 + gradcorr_nucl(j,i)=0.0d0 + gradcorr3_nucl(j,i)=0.0d0 + gradxorr_nucl(j,i)=0.0d0 + gradxorr3_nucl(j,i)=0.0d0 + gelsbx(j,i)=0.0d0 + gsbloc(j,i)=0.0d0 + gsblocx(j,i)=0.0d0 + gradpepcat(j,i)=0.0d0 + gradpepcatx(j,i)=0.0d0 + gradcatcat(j,i)=0.0d0 + gvdwx_scbase(j,i)=0.0d0 + gvdwc_scbase(j,i)=0.0d0 + gvdwx_pepbase(j,i)=0.0d0 + gvdwc_pepbase(j,i)=0.0d0 + gvdwx_scpho(j,i)=0.0d0 + gvdwc_scpho(j,i)=0.0d0 + gvdwc_peppho(j,i)=0.0d0 + enddo + enddo + do i=0,nres + do j=1,3 + do intertyp=1,3 + gloc_sc(intertyp,i,icg)=0.0d0 + enddo + enddo + enddo + do i=1,nres + do j=1,maxcontsshi + shield_list(j,i)=0 + do k=1,3 + !C print *,i,j,k + grad_shield_side(k,j,i)=0.0d0 + grad_shield_loc(k,j,i)=0.0d0 + enddo + enddo + ishield_list(i)=0 + enddo - do i=1,4*nres - gloc(i,icg)=0.0D0 - enddo - do i=1,nres - gel_loc_loc(i)=0.0d0 - gcorr_loc(i)=0.0d0 - g_corr5_loc(i)=0.0d0 - g_corr6_loc(i)=0.0d0 - gel_loc_turn3(i)=0.0d0 - gel_loc_turn4(i)=0.0d0 - gel_loc_turn6(i)=0.0d0 - gsccor_loc(i)=0.0d0 - enddo -! initialize gcart and gxcart -! allocate(gcart(3,0:nres),gxcart(3,0:nres)) !(3,0:MAXRES) - do i=0,nres - do j=1,3 - gcart(j,i)=0.0d0 - gxcart(j,i)=0.0d0 - enddo - enddo - return - end subroutine zerograd -!----------------------------------------------------------------------------- - real(kind=8) function fdum() - fdum=0.0D0 - return - end function fdum -!----------------------------------------------------------------------------- -! intcartderiv.F -!----------------------------------------------------------------------------- - subroutine intcartderiv -! implicit real*8 (a-h,o-z) -! include 'DIMENSIONS' + ! + ! Initialize the gradient of local energy terms. + ! + ! allocate(gloc(4*nres,2)) !!(maxvar,2)(maxvar=6*maxres) + ! if (.not.allocated(gel_loc_loc)) allocate(gel_loc_loc(nres)) !(maxvar)(maxvar=6*maxres) + ! if (.not.allocated(gcorr_loc)) allocate(gcorr_loc(nres)) !(maxvar)(maxvar=6*maxres) + ! allocate(g_corr5_loc(nres),g_corr6_loc(nres)) !(maxvar)(maxvar=6*maxres) + ! allocate(gel_loc_turn3(nres)) + ! allocate(gel_loc_turn4(nres),gel_loc_turn6(nres)) !(maxvar)(maxvar=6*maxres) + ! allocate(gsccor_loc(nres)) !(maxres) + + do i=1,4*nres + gloc(i,icg)=0.0D0 + enddo + do i=1,nres + gel_loc_loc(i)=0.0d0 + gcorr_loc(i)=0.0d0 + g_corr5_loc(i)=0.0d0 + g_corr6_loc(i)=0.0d0 + gel_loc_turn3(i)=0.0d0 + gel_loc_turn4(i)=0.0d0 + gel_loc_turn6(i)=0.0d0 + gsccor_loc(i)=0.0d0 + enddo + ! initialize gcart and gxcart + ! allocate(gcart(3,0:nres),gxcart(3,0:nres)) !(3,0:MAXRES) + do i=0,nres + do j=1,3 + gcart(j,i)=0.0d0 + gxcart(j,i)=0.0d0 + enddo + enddo + return + end subroutine zerograd + !----------------------------------------------------------------------------- + real(kind=8) function fdum() + fdum=0.0D0 + return + end function fdum + !----------------------------------------------------------------------------- + ! intcartderiv.F + !----------------------------------------------------------------------------- + subroutine intcartderiv + ! implicit real*8 (a-h,o-z) + ! include 'DIMENSIONS' #ifdef MPI - include 'mpif.h' + include 'mpif.h' #endif -! include 'COMMON.SETUP' -! include 'COMMON.CHAIN' -! include 'COMMON.VAR' -! include 'COMMON.GEO' -! include 'COMMON.INTERACT' -! include 'COMMON.DERIV' -! include 'COMMON.IOUNITS' -! include 'COMMON.LOCAL' -! include 'COMMON.SCCOR' - real(kind=8) :: pi4,pi34 - real(kind=8),dimension(3,2,nres) :: dcostheta ! (3,2,maxres) - real(kind=8),dimension(3,3,nres) :: dcosphi,dsinphi,dcosalpha,& - dcosomega,dsinomega !(3,3,maxres) - real(kind=8),dimension(3) :: vo1,vo2,vo3,dummy,vp1,vp2,vp3,vpp1,n - - integer :: i,j,k - real(kind=8) :: cost,sint,cost1,sint1,cost2,sint2,sing,cosg,scalp,& - fac0,fac1,fac2,fac3,fac4,fac5,fac6,ctgt,ctgt1,cosg_inv,& - fac7,fac8,fac9,scala1,scala2,cosa,sina,sino,fac15,fac16,& - fac17,coso_inv,fac10,fac11,fac12,fac13,fac14 - integer :: nres2 - nres2=2*nres + ! include 'COMMON.SETUP' + ! include 'COMMON.CHAIN' + ! include 'COMMON.VAR' + ! include 'COMMON.GEO' + ! include 'COMMON.INTERACT' + ! include 'COMMON.DERIV' + ! include 'COMMON.IOUNITS' + ! include 'COMMON.LOCAL' + ! include 'COMMON.SCCOR' + real(kind=8) :: pi4,pi34 + real(kind=8),dimension(3,2,nres) :: dcostheta ! (3,2,maxres) + real(kind=8),dimension(3,3,nres) :: dcosphi,dsinphi,dcosalpha,& + dcosomega,dsinomega !(3,3,maxres) + real(kind=8),dimension(3) :: vo1,vo2,vo3,dummy,vp1,vp2,vp3,vpp1,n + + integer :: i,j,k + real(kind=8) :: cost,sint,cost1,sint1,cost2,sint2,sing,cosg,scalp,& + fac0,fac1,fac2,fac3,fac4,fac5,fac6,ctgt,ctgt1,cosg_inv,& + fac7,fac8,fac9,scala1,scala2,cosa,sina,sino,fac15,fac16,& + fac17,coso_inv,fac10,fac11,fac12,fac13,fac14 + integer :: nres2 + nres2=2*nres -!el from module energy------------- -!el allocate(dcostau(3,3,3,itau_start:itau_end)) !(3,3,3,maxres2)maxres2=2*maxres -!el allocate(dsintau(3,3,3,itau_start:itau_end)) -!el allocate(dtauangle(3,3,3,itau_start:itau_end)) + !el from module energy------------- + !el allocate(dcostau(3,3,3,itau_start:itau_end)) !(3,3,3,maxres2)maxres2=2*maxres + !el allocate(dsintau(3,3,3,itau_start:itau_end)) + !el allocate(dtauangle(3,3,3,itau_start:itau_end)) -!el allocate(dcostau(3,3,3,0:nres2)) !(3,3,3,maxres2)maxres2=2*maxres -!el allocate(dsintau(3,3,3,0:nres2)) -!el allocate(dtauangle(3,3,3,0:nres2)) -!el allocate(domicron(3,2,2,0:nres2)) -!el allocate(dcosomicron(3,2,2,0:nres2)) + !el allocate(dcostau(3,3,3,0:nres2)) !(3,3,3,maxres2)maxres2=2*maxres + !el allocate(dsintau(3,3,3,0:nres2)) + !el allocate(dtauangle(3,3,3,0:nres2)) + !el allocate(domicron(3,2,2,0:nres2)) + !el allocate(dcosomicron(3,2,2,0:nres2)) #if defined(MPI) && defined(PARINTDER) - if (nfgtasks.gt.1 .and. me.eq.king) & - call MPI_Bcast(8,1,MPI_INTEGER,king,FG_COMM,IERROR) + if (nfgtasks.gt.1 .and. me.eq.king) & + call MPI_Bcast(8,1,MPI_INTEGER,king,FG_COMM,IERROR) #endif - pi4 = 0.5d0*pipol - pi34 = 3*pi4 + pi4 = 0.5d0*pipol + pi34 = 3*pi4 -! allocate(dtheta(3,2,nres)) !(3,2,maxres) -! allocate(dphi(3,3,nres),dalpha(3,3,nres),domega(3,3,nres)) !(3,3,maxres) + ! allocate(dtheta(3,2,nres)) !(3,2,maxres) + ! allocate(dphi(3,3,nres),dalpha(3,3,nres),domega(3,3,nres)) !(3,3,maxres) -! write (iout,*) "iphi1_start",iphi1_start," iphi1_end",iphi1_end - do i=1,nres - do j=1,3 - dtheta(j,1,i)=0.0d0 - dtheta(j,2,i)=0.0d0 - dphi(j,1,i)=0.0d0 - dphi(j,2,i)=0.0d0 - dphi(j,3,i)=0.0d0 - enddo - enddo -! Derivatives of theta's + ! write (iout,*) "iphi1_start",iphi1_start," iphi1_end",iphi1_end + do i=1,nres + do j=1,3 + dtheta(j,1,i)=0.0d0 + dtheta(j,2,i)=0.0d0 + dphi(j,1,i)=0.0d0 + dphi(j,2,i)=0.0d0 + dphi(j,3,i)=0.0d0 + enddo + enddo + ! Derivatives of theta's #if defined(MPI) && defined(PARINTDER) -! We need dtheta(:,:,i-1) to compute dphi(:,:,i) - do i=max0(ithet_start-1,3),ithet_end + ! We need dtheta(:,:,i-1) to compute dphi(:,:,i) + do i=max0(ithet_start-1,3),ithet_end #else - do i=3,nres + do i=3,nres #endif - cost=dcos(theta(i)) - sint=sqrt(1-cost*cost) - do j=1,3 - dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/& - vbld(i-1) - if (itype(i-1).ne.ntyp1) dtheta(j,1,i)=-dcostheta(j,1,i)/sint - dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/& - vbld(i) - if (itype(i-1).ne.ntyp1) dtheta(j,2,i)=-dcostheta(j,2,i)/sint - enddo - enddo + cost=dcos(theta(i)) + sint=sqrt(1-cost*cost) + do j=1,3 + dcostheta(j,1,i)=-(dc_norm(j,i-1)+cost*dc_norm(j,i-2))/& + vbld(i-1) + if (itype(i-1,1).ne.ntyp1) dtheta(j,1,i)=-dcostheta(j,1,i)/sint + dcostheta(j,2,i)=-(dc_norm(j,i-2)+cost*dc_norm(j,i-1))/& + vbld(i) + if (itype(i-1,1).ne.ntyp1) dtheta(j,2,i)=-dcostheta(j,2,i)/sint + enddo + enddo #if defined(MPI) && defined(PARINTDER) -! We need dtheta(:,:,i-1) to compute dphi(:,:,i) - do i=max0(ithet_start-1,3),ithet_end + ! We need dtheta(:,:,i-1) to compute dphi(:,:,i) + do i=max0(ithet_start-1,3),ithet_end #else - do i=3,nres + do i=3,nres #endif - if ((itype(i-1).ne.10).and.(itype(i-1).ne.ntyp1)) then - cost1=dcos(omicron(1,i)) - sint1=sqrt(1-cost1*cost1) - cost2=dcos(omicron(2,i)) - sint2=sqrt(1-cost2*cost2) - do j=1,3 -!C Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1) - dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+ & - cost1*dc_norm(j,i-2))/ & - vbld(i-1) - domicron(j,1,1,i)=-1/sint1*dcosomicron(j,1,1,i) - dcosomicron(j,1,2,i)=-(dc_norm(j,i-2) & - +cost1*(dc_norm(j,i-1+nres)))/ & - vbld(i-1+nres) - domicron(j,1,2,i)=-1/sint1*dcosomicron(j,1,2,i) -!C Calculate derivative over second omicron Sci-1,Cai-1 Cai -!C Looks messy but better than if in loop - dcosomicron(j,2,1,i)=-(-dc_norm(j,i-1+nres) & - +cost2*dc_norm(j,i-1))/ & - vbld(i) - domicron(j,2,1,i)=-1/sint2*dcosomicron(j,2,1,i) - dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) & - +cost2*(-dc_norm(j,i-1+nres)))/ & - vbld(i-1+nres) -! write(iout,*) "vbld", i,itype(i),vbld(i-1+nres) - domicron(j,2,2,i)=-1/sint2*dcosomicron(j,2,2,i) - enddo - endif - enddo -!elwrite(iout,*) "after vbld write" -! Derivatives of phi: -! If phi is 0 or 180 degrees, then the formulas -! have to be derived by power series expansion of the -! conventional formulas around 0 and 180. + if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1)) then + cost1=dcos(omicron(1,i)) + sint1=sqrt(1-cost1*cost1) + cost2=dcos(omicron(2,i)) + sint2=sqrt(1-cost2*cost2) + do j=1,3 + !C Calculate derivative over first omicron (Cai-2,Cai-1,SCi-1) + dcosomicron(j,1,1,i)=-(dc_norm(j,i-1+nres)+ & + cost1*dc_norm(j,i-2))/ & + vbld(i-1) + domicron(j,1,1,i)=-1/sint1*dcosomicron(j,1,1,i) + dcosomicron(j,1,2,i)=-(dc_norm(j,i-2) & + +cost1*(dc_norm(j,i-1+nres)))/ & + vbld(i-1+nres) + domicron(j,1,2,i)=-1/sint1*dcosomicron(j,1,2,i) + !C Calculate derivative over second omicron Sci-1,Cai-1 Cai + !C Looks messy but better than if in loop + dcosomicron(j,2,1,i)=-(-dc_norm(j,i-1+nres) & + +cost2*dc_norm(j,i-1))/ & + vbld(i) + domicron(j,2,1,i)=-1/sint2*dcosomicron(j,2,1,i) + dcosomicron(j,2,2,i)=-(dc_norm(j,i-1) & + +cost2*(-dc_norm(j,i-1+nres)))/ & + vbld(i-1+nres) + ! write(iout,*) "vbld", i,itype(i,1),vbld(i-1+nres) + domicron(j,2,2,i)=-1/sint2*dcosomicron(j,2,2,i) + enddo + endif + enddo + !elwrite(iout,*) "after vbld write" + ! Derivatives of phi: + ! If phi is 0 or 180 degrees, then the formulas + ! have to be derived by power series expansion of the + ! conventional formulas around 0 and 180. #ifdef PARINTDER - do i=iphi1_start,iphi1_end + do i=iphi1_start,iphi1_end #else - do i=4,nres + do i=4,nres #endif -! if (itype(i-1).eq.21 .or. itype(i-2).eq.21 ) cycle -! the conventional case - sint=dsin(theta(i)) - sint1=dsin(theta(i-1)) - sing=dsin(phi(i)) - cost=dcos(theta(i)) - cost1=dcos(theta(i-1)) - cosg=dcos(phi(i)) - scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1)) - fac0=1.0d0/(sint1*sint) - fac1=cost*fac0 - fac2=cost1*fac0 - fac3=cosg*cost1/(sint1*sint1) - fac4=cosg*cost/(sint*sint) -! Obtaining the gamma derivatives from sine derivative - if (phi(i).gt.-pi4.and.phi(i).le.pi4.or. & - phi(i).gt.pi34.and.phi(i).le.pi.or. & - phi(i).ge.-pi.and.phi(i).le.-pi34) then - call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) - call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2) - call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) - do j=1,3 - ctgt=cost/sint - ctgt1=cost1/sint1 - cosg_inv=1.0d0/cosg - if (itype(i-1).ne.ntyp1 .and. itype(i-2).ne.ntyp1) then - dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) & - -(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2) - dphi(j,1,i)=cosg_inv*dsinphi(j,1,i) - dsinphi(j,2,i)= & - -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*dtheta(j,1,i)) & - -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) - dphi(j,2,i)=cosg_inv*dsinphi(j,2,i) - dsinphi(j,3,i)=-sing*ctgt*dtheta(j,2,i) & - +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) -! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) - dphi(j,3,i)=cosg_inv*dsinphi(j,3,i) - endif -! Bug fixed 3/24/05 (AL) - enddo -! Obtaining the gamma derivatives from cosine derivative - else - do j=1,3 - if (itype(i-1).ne.ntyp1 .and. itype(i-2).ne.ntyp1) then - dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* & - dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* & - dc_norm(j,i-3))/vbld(i-2) - dphi(j,1,i)=-1/sing*dcosphi(j,1,i) - dcosphi(j,2,i)=fac1*dcostheta(j,2,i-1)+fac2* & - dcostheta(j,1,i)+fac3*dcostheta(j,2,i-1)+fac4* & - dcostheta(j,1,i) - dphi(j,2,i)=-1/sing*dcosphi(j,2,i) - dcosphi(j,3,i)=fac2*dcostheta(j,2,i)+fac4* & - dcostheta(j,2,i)-fac0*(dc_norm(j,i-3)-scalp* & - dc_norm(j,i-1))/vbld(i) - dphi(j,3,i)=-1/sing*dcosphi(j,3,i) - endif - enddo - endif - enddo -!alculate derivative of Tauangle + ! if (itype(i-1,1).eq.21 .or. itype(i-2,1).eq.21 ) cycle + ! the conventional case + sint=dsin(theta(i)) + sint1=dsin(theta(i-1)) + sing=dsin(phi(i)) + cost=dcos(theta(i)) + cost1=dcos(theta(i-1)) + cosg=dcos(phi(i)) + scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) + ! Obtaining the gamma derivatives from sine derivative + if (phi(i).gt.-pi4.and.phi(i).le.pi4.or. & + phi(i).gt.pi34.and.phi(i).le.pi.or. & + phi(i).ge.-pi.and.phi(i).le.-pi34) then + call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-1),vp2) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then + dsinphi(j,1,i)=-sing*ctgt1*dtheta(j,1,i-1) & + -(fac0*vp1(j)+sing*dc_norm(j,i-3))*vbld_inv(i-2) + dphi(j,1,i)=cosg_inv*dsinphi(j,1,i) + dsinphi(j,2,i)= & + -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*dtheta(j,1,i)) & + -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dphi(j,2,i)=cosg_inv*dsinphi(j,2,i) + dsinphi(j,3,i)=-sing*ctgt*dtheta(j,2,i) & + +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) + ! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dphi(j,3,i)=cosg_inv*dsinphi(j,3,i) + endif + ! Bug fixed 3/24/05 (AL) + enddo + ! Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then + dcosphi(j,1,i)=fac1*dcostheta(j,1,i-1)+fac3* & + dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1)-scalp* & + dc_norm(j,i-3))/vbld(i-2) + dphi(j,1,i)=-1/sing*dcosphi(j,1,i) + dcosphi(j,2,i)=fac1*dcostheta(j,2,i-1)+fac2* & + dcostheta(j,1,i)+fac3*dcostheta(j,2,i-1)+fac4* & + dcostheta(j,1,i) + dphi(j,2,i)=-1/sing*dcosphi(j,2,i) + dcosphi(j,3,i)=fac2*dcostheta(j,2,i)+fac4* & + dcostheta(j,2,i)-fac0*(dc_norm(j,i-3)-scalp* & + dc_norm(j,i-1))/vbld(i) + dphi(j,3,i)=-1/sing*dcosphi(j,3,i) + endif + enddo + endif + enddo + !alculate derivative of Tauangle #ifdef PARINTDER - do i=itau_start,itau_end + do i=itau_start,itau_end #else - do i=3,nres -!elwrite(iout,*) " vecpr",i,nres + do i=3,nres + !elwrite(iout,*) " vecpr",i,nres #endif - if ((itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10)) cycle -! if ((itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10).or. -! & (itype(i-1).eq.ntyp1).or.(itype(i).eq.ntyp1)) cycle -!c dtauangle(j,intertyp,dervityp,residue number) -!c INTERTYP=1 SC...Ca...Ca..Ca -! the conventional case - sint=dsin(theta(i)) - sint1=dsin(omicron(2,i-1)) - sing=dsin(tauangle(1,i)) - cost=dcos(theta(i)) - cost1=dcos(omicron(2,i-1)) - cosg=dcos(tauangle(1,i)) -!elwrite(iout,*) " vecpr5",i,nres - do j=1,3 -!elwrite(iout,*) " vecpreee",i,nres,j,i-2+nres -!elwrite(iout,*) " vecpr5",dc_norm2(1,1) - dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) -! write(iout,*) dc_norm2(j,i-2+nres),"dcnorm" - enddo - scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1)) - fac0=1.0d0/(sint1*sint) - fac1=cost*fac0 - fac2=cost1*fac0 - fac3=cosg*cost1/(sint1*sint1) - fac4=cosg*cost/(sint*sint) -! write(iout,*) "faki",fac0,fac1,fac2,fac3,fac4 -! Obtaining the gamma derivatives from sine derivative - if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or. & - tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or. & - tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then - call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) - call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2) - call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) - do j=1,3 - ctgt=cost/sint - ctgt1=cost1/sint1 - cosg_inv=1.0d0/cosg - dsintau(j,1,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) & - -(fac0*vp1(j)+sing*(dc_norm2(j,i-2+nres))) & - *vbld_inv(i-2+nres) - dtauangle(j,1,1,i)=cosg_inv*dsintau(j,1,1,i) - dsintau(j,1,2,i)= & - -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*dtheta(j,1,i)) & - -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) -! write(iout,*) "dsintau", dsintau(j,1,2,i) - dtauangle(j,1,2,i)=cosg_inv*dsintau(j,1,2,i) -! Bug fixed 3/24/05 (AL) - dsintau(j,1,3,i)=-sing*ctgt*dtheta(j,2,i) & - +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) -! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) - dtauangle(j,1,3,i)=cosg_inv*dsintau(j,1,3,i) - enddo -! Obtaining the gamma derivatives from cosine derivative - else - do j=1,3 - dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* & - dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp* & - (dc_norm2(j,i-2+nres)))/vbld(i-2+nres) - dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i) - dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* & - dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* & - dcostheta(j,1,i) - dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i) - dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4* & - dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp* & - dc_norm(j,i-1))/vbld(i) - dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i) -! write (iout,*) "else",i - enddo - endif -! do k=1,3 -! write(iout,*) "tu",i,k,(dtauangle(j,1,k,i),j=1,3) -! enddo - enddo -!C Second case Ca...Ca...Ca...SC + if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle + ! if ((itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10).or. + ! & (itype(i-1,1).eq.ntyp1).or.(itype(i,1).eq.ntyp1)) cycle + !c dtauangle(j,intertyp,dervityp,residue number) + !c INTERTYP=1 SC...Ca...Ca..Ca + ! the conventional case + sint=dsin(theta(i)) + sint1=dsin(omicron(2,i-1)) + sing=dsin(tauangle(1,i)) + cost=dcos(theta(i)) + cost1=dcos(omicron(2,i-1)) + cosg=dcos(tauangle(1,i)) + !elwrite(iout,*) " vecpr5",i,nres + do j=1,3 + !elwrite(iout,*) " vecpreee",i,nres,j,i-2+nres + !elwrite(iout,*) " vecpr5",dc_norm2(1,1) + dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) + ! write(iout,*) dc_norm2(j,i-2+nres),"dcnorm" + enddo + scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) + ! write(iout,*) "faki",fac0,fac1,fac2,fac3,fac4 + ! Obtaining the gamma derivatives from sine derivative + if (tauangle(1,i).gt.-pi4.and.tauangle(1,i).le.pi4.or. & + tauangle(1,i).gt.pi34.and.tauangle(1,i).le.pi.or. & + tauangle(1,i).gt.-pi.and.tauangle(1,i).le.-pi34) then + call vecpr(dc_norm(1,i-1),dc_norm(1,i-2),vp1) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1),vp2) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,1,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) & + -(fac0*vp1(j)+sing*(dc_norm2(j,i-2+nres))) & + *vbld_inv(i-2+nres) + dtauangle(j,1,1,i)=cosg_inv*dsintau(j,1,1,i) + dsintau(j,1,2,i)= & + -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*dtheta(j,1,i)) & + -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + ! write(iout,*) "dsintau", dsintau(j,1,2,i) + dtauangle(j,1,2,i)=cosg_inv*dsintau(j,1,2,i) + ! Bug fixed 3/24/05 (AL) + dsintau(j,1,3,i)=-sing*ctgt*dtheta(j,2,i) & + +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i) + ! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,1,3,i)=cosg_inv*dsintau(j,1,3,i) + enddo + ! Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,1,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* & + dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1)-scalp* & + (dc_norm2(j,i-2+nres)))/vbld(i-2+nres) + dtauangle(j,1,1,i)=-1/sing*dcostau(j,1,1,i) + dcostau(j,1,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* & + dcostheta(j,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* & + dcostheta(j,1,i) + dtauangle(j,1,2,i)=-1/sing*dcostau(j,1,2,i) + dcostau(j,1,3,i)=fac2*dcostheta(j,2,i)+fac4* & + dcostheta(j,2,i)-fac0*(-dc_norm(j,i-2+nres)-scalp* & + dc_norm(j,i-1))/vbld(i) + dtauangle(j,1,3,i)=-1/sing*dcostau(j,1,3,i) + ! write (iout,*) "else",i + enddo + endif + ! do k=1,3 + ! write(iout,*) "tu",i,k,(dtauangle(j,1,k,i),j=1,3) + ! enddo + enddo + !C Second case Ca...Ca...Ca...SC #ifdef PARINTDER - do i=itau_start,itau_end + do i=itau_start,itau_end #else - do i=4,nres + do i=4,nres #endif - if ((itype(i-1).eq.ntyp1).or.(itype(i-1).eq.10).or. & - (itype(i-2).eq.ntyp1).or.(itype(i-3).eq.ntyp1)) cycle -! the conventional case - sint=dsin(omicron(1,i)) - sint1=dsin(theta(i-1)) - sing=dsin(tauangle(2,i)) - cost=dcos(omicron(1,i)) - cost1=dcos(theta(i-1)) - cosg=dcos(tauangle(2,i)) -! do j=1,3 -! dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) -! enddo - scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1+nres)) - fac0=1.0d0/(sint1*sint) - fac1=cost*fac0 - fac2=cost1*fac0 - fac3=cosg*cost1/(sint1*sint1) - fac4=cosg*cost/(sint*sint) -! Obtaining the gamma derivatives from sine derivative - if (tauangle(2,i).gt.-pi4.and.tauangle(2,i).le.pi4.or. & - tauangle(2,i).gt.pi34.and.tauangle(2,i).le.pi.or. & - tauangle(2,i).gt.-pi.and.tauangle(2,i).le.-pi34) then - call vecpr(dc_norm2(1,i-1+nres),dc_norm(1,i-2),vp1) - call vecpr(dc_norm(1,i-3),dc_norm(1,i-1+nres),vp2) - call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) - do j=1,3 - ctgt=cost/sint - ctgt1=cost1/sint1 - cosg_inv=1.0d0/cosg - dsintau(j,2,1,i)=-sing*ctgt1*dtheta(j,1,i-1) & - +(fac0*vp1(j)-sing*dc_norm(j,i-3))*vbld_inv(i-2) -! write(iout,*) i,j,dsintau(j,2,1,i),sing*ctgt1*dtheta(j,1,i-1), -! &fac0*vp1(j),sing*dc_norm(j,i-3),vbld_inv(i-2),"dsintau(2,1)" - dtauangle(j,2,1,i)=cosg_inv*dsintau(j,2,1,i) - dsintau(j,2,2,i)= & - -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*domicron(j,1,1,i)) & - -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) -! write(iout,*) "sprawdzenie",i,j,sing*ctgt1*dtheta(j,2,i-1), -! & sing*ctgt*domicron(j,1,2,i), -! & (fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) - dtauangle(j,2,2,i)=cosg_inv*dsintau(j,2,2,i) -! Bug fixed 3/24/05 (AL) - dsintau(j,2,3,i)=-sing*ctgt*domicron(j,1,2,i) & - +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres))*vbld_inv(i-1+nres) -! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) - dtauangle(j,2,3,i)=cosg_inv*dsintau(j,2,3,i) - enddo -! Obtaining the gamma derivatives from cosine derivative - else - do j=1,3 - dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3* & - dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* & - dc_norm(j,i-3))/vbld(i-2) - dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i) - dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2* & - dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4* & - dcosomicron(j,1,1,i) - dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i) - dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* & - dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp* & - dc_norm(j,i-1+nres))/vbld(i-1+nres) - dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i) -! write(iout,*) i,j,"else", dtauangle(j,2,3,i) - enddo - endif - enddo + if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. & + (itype(i-2,1).eq.ntyp1).or.(itype(i-3,1).eq.ntyp1)) cycle + ! the conventional case + sint=dsin(omicron(1,i)) + sint1=dsin(theta(i-1)) + sing=dsin(tauangle(2,i)) + cost=dcos(omicron(1,i)) + cost1=dcos(theta(i-1)) + cosg=dcos(tauangle(2,i)) + ! do j=1,3 + ! dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) + ! enddo + scalp=scalar(dc_norm(1,i-3),dc_norm(1,i-1+nres)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) + ! Obtaining the gamma derivatives from sine derivative + if (tauangle(2,i).gt.-pi4.and.tauangle(2,i).le.pi4.or. & + tauangle(2,i).gt.pi34.and.tauangle(2,i).le.pi.or. & + tauangle(2,i).gt.-pi.and.tauangle(2,i).le.-pi34) then + call vecpr(dc_norm2(1,i-1+nres),dc_norm(1,i-2),vp1) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-1+nres),vp2) + call vecpr(dc_norm(1,i-3),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,2,1,i)=-sing*ctgt1*dtheta(j,1,i-1) & + +(fac0*vp1(j)-sing*dc_norm(j,i-3))*vbld_inv(i-2) + ! write(iout,*) i,j,dsintau(j,2,1,i),sing*ctgt1*dtheta(j,1,i-1), + ! &fac0*vp1(j),sing*dc_norm(j,i-3),vbld_inv(i-2),"dsintau(2,1)" + dtauangle(j,2,1,i)=cosg_inv*dsintau(j,2,1,i) + dsintau(j,2,2,i)= & + -sing*(ctgt1*dtheta(j,2,i-1)+ctgt*domicron(j,1,1,i)) & + -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + ! write(iout,*) "sprawdzenie",i,j,sing*ctgt1*dtheta(j,2,i-1), + ! & sing*ctgt*domicron(j,1,2,i), + ! & (fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dtauangle(j,2,2,i)=cosg_inv*dsintau(j,2,2,i) + ! Bug fixed 3/24/05 (AL) + dsintau(j,2,3,i)=-sing*ctgt*domicron(j,1,2,i) & + +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres))*vbld_inv(i-1+nres) + ! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,2,3,i)=cosg_inv*dsintau(j,2,3,i) + enddo + ! Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,2,1,i)=fac1*dcostheta(j,1,i-1)+fac3* & + dcostheta(j,1,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* & + dc_norm(j,i-3))/vbld(i-2) + dtauangle(j,2,1,i)=-1/sing*dcostau(j,2,1,i) + dcostau(j,2,2,i)=fac1*dcostheta(j,2,i-1)+fac2* & + dcosomicron(j,1,1,i)+fac3*dcostheta(j,2,i-1)+fac4* & + dcosomicron(j,1,1,i) + dtauangle(j,2,2,i)=-1/sing*dcostau(j,2,2,i) + dcostau(j,2,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* & + dcosomicron(j,1,2,i)-fac0*(dc_norm(j,i-3)-scalp* & + dc_norm(j,i-1+nres))/vbld(i-1+nres) + dtauangle(j,2,3,i)=-1/sing*dcostau(j,2,3,i) + ! write(iout,*) i,j,"else", dtauangle(j,2,3,i) + enddo + endif + enddo -!CC third case SC...Ca...Ca...SC + !CC third case SC...Ca...Ca...SC #ifdef PARINTDER - do i=itau_start,itau_end + do i=itau_start,itau_end #else - do i=3,nres + do i=3,nres #endif -! the conventional case - if ((itype(i-1).eq.ntyp1).or.(itype(i-1).eq.10).or. & - (itype(i-2).eq.ntyp1).or.(itype(i-2).eq.10)) cycle - sint=dsin(omicron(1,i)) - sint1=dsin(omicron(2,i-1)) - sing=dsin(tauangle(3,i)) - cost=dcos(omicron(1,i)) - cost1=dcos(omicron(2,i-1)) - cosg=dcos(tauangle(3,i)) - do j=1,3 - dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) -! dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) - enddo - scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres)) - fac0=1.0d0/(sint1*sint) - fac1=cost*fac0 - fac2=cost1*fac0 - fac3=cosg*cost1/(sint1*sint1) - fac4=cosg*cost/(sint*sint) -! Obtaining the gamma derivatives from sine derivative - if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or. & - tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or. & - tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then - call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1) - call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2) - call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) - do j=1,3 - ctgt=cost/sint - ctgt1=cost1/sint1 - cosg_inv=1.0d0/cosg - dsintau(j,3,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) & - -(fac0*vp1(j)-sing*dc_norm(j,i-2+nres)) & - *vbld_inv(i-2+nres) - dtauangle(j,3,1,i)=cosg_inv*dsintau(j,3,1,i) - dsintau(j,3,2,i)= & - -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*domicron(j,1,1,i)) & - -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) - dtauangle(j,3,2,i)=cosg_inv*dsintau(j,3,2,i) -! Bug fixed 3/24/05 (AL) - dsintau(j,3,3,i)=-sing*ctgt*domicron(j,1,2,i) & - +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres)) & - *vbld_inv(i-1+nres) -! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) - dtauangle(j,3,3,i)=cosg_inv*dsintau(j,3,3,i) - enddo -! Obtaining the gamma derivatives from cosine derivative - else - do j=1,3 - dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* & - dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* & - dc_norm2(j,i-2+nres))/vbld(i-2+nres) - dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i) - dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* & - dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* & - dcosomicron(j,1,1,i) - dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i) - dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* & - dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp* & - dc_norm(j,i-1+nres))/vbld(i-1+nres) - dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i) -! write(iout,*) "else",i - enddo - endif - enddo + ! the conventional case + if ((itype(i-1,1).eq.ntyp1).or.(itype(i-1,1).eq.10).or. & + (itype(i-2,1).eq.ntyp1).or.(itype(i-2,1).eq.10)) cycle + sint=dsin(omicron(1,i)) + sint1=dsin(omicron(2,i-1)) + sing=dsin(tauangle(3,i)) + cost=dcos(omicron(1,i)) + cost1=dcos(omicron(2,i-1)) + cosg=dcos(tauangle(3,i)) + do j=1,3 + dc_norm2(j,i-2+nres)=-dc_norm(j,i-2+nres) + ! dc_norm2(j,i-1+nres)=-dc_norm(j,i-1+nres) + enddo + scalp=scalar(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres)) + fac0=1.0d0/(sint1*sint) + fac1=cost*fac0 + fac2=cost1*fac0 + fac3=cosg*cost1/(sint1*sint1) + fac4=cosg*cost/(sint*sint) + ! Obtaining the gamma derivatives from sine derivative + if (tauangle(3,i).gt.-pi4.and.tauangle(3,i).le.pi4.or. & + tauangle(3,i).gt.pi34.and.tauangle(3,i).le.pi.or. & + tauangle(3,i).gt.-pi.and.tauangle(3,i).le.-pi34) then + call vecpr(dc_norm(1,i-1+nres),dc_norm(1,i-2),vp1) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-1+nres),vp2) + call vecpr(dc_norm2(1,i-2+nres),dc_norm(1,i-2),vp3) + do j=1,3 + ctgt=cost/sint + ctgt1=cost1/sint1 + cosg_inv=1.0d0/cosg + dsintau(j,3,1,i)=-sing*ctgt1*domicron(j,2,2,i-1) & + -(fac0*vp1(j)-sing*dc_norm(j,i-2+nres)) & + *vbld_inv(i-2+nres) + dtauangle(j,3,1,i)=cosg_inv*dsintau(j,3,1,i) + dsintau(j,3,2,i)= & + -sing*(ctgt1*domicron(j,2,1,i-1)+ctgt*domicron(j,1,1,i)) & + -(fac0*vp2(j)+sing*dc_norm(j,i-2))*vbld_inv(i-1) + dtauangle(j,3,2,i)=cosg_inv*dsintau(j,3,2,i) + ! Bug fixed 3/24/05 (AL) + dsintau(j,3,3,i)=-sing*ctgt*domicron(j,1,2,i) & + +(fac0*vp3(j)-sing*dc_norm(j,i-1+nres)) & + *vbld_inv(i-1+nres) + ! & +(fac0*vp3(j)-sing*dc_norm(j,i-1))*vbld_inv(i-1) + dtauangle(j,3,3,i)=cosg_inv*dsintau(j,3,3,i) + enddo + ! Obtaining the gamma derivatives from cosine derivative + else + do j=1,3 + dcostau(j,3,1,i)=fac1*dcosomicron(j,2,2,i-1)+fac3* & + dcosomicron(j,2,2,i-1)-fac0*(dc_norm(j,i-1+nres)-scalp* & + dc_norm2(j,i-2+nres))/vbld(i-2+nres) + dtauangle(j,3,1,i)=-1/sing*dcostau(j,3,1,i) + dcostau(j,3,2,i)=fac1*dcosomicron(j,2,1,i-1)+fac2* & + dcosomicron(j,1,1,i)+fac3*dcosomicron(j,2,1,i-1)+fac4* & + dcosomicron(j,1,1,i) + dtauangle(j,3,2,i)=-1/sing*dcostau(j,3,2,i) + dcostau(j,3,3,i)=fac2*dcosomicron(j,1,2,i)+fac4* & + dcosomicron(j,1,2,i)-fac0*(dc_norm2(j,i-2+nres)-scalp* & + dc_norm(j,i-1+nres))/vbld(i-1+nres) + dtauangle(j,3,3,i)=-1/sing*dcostau(j,3,3,i) + ! write(iout,*) "else",i + enddo + endif + enddo #ifdef CRYST_SC -! Derivatives of side-chain angles alpha and omega + ! Derivatives of side-chain angles alpha and omega #if defined(MPI) && defined(PARINTDER) - do i=ibond_start,ibond_end + do i=ibond_start,ibond_end #else - do i=2,nres-1 + do i=2,nres-1 #endif - if(itype(i).ne.10 .and. itype(i).ne.ntyp1) then - fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1)))) - fac6=fac5/vbld(i) - fac7=fac5*fac5 - fac8=fac5/vbld(i+1) - fac9=fac5/vbld(i+nres) - scala1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres)) - scala2=scalar(dc_norm(1,i),dc_norm(1,i+nres)) - cosa=dsqrt(0.5d0/(1.0d0+dcos(theta(i+1))))* & - (scalar(dC_norm(1,i),dC_norm(1,i+nres)) & - -scalar(dC_norm(1,i-1),dC_norm(1,i+nres))) - sina=sqrt(1-cosa*cosa) - sino=dsin(omeg(i)) -! write (iout,*) "i",i," cosa",cosa," sina",sina," sino",sino - do j=1,3 - dcosalpha(j,1,i)=fac6*(scala1*dc_norm(j,i-1)- & - dc_norm(j,i+nres))-cosa*fac7*dcostheta(j,1,i+1) - dalpha(j,1,i)=-1/sina*dcosalpha(j,1,i) - dcosalpha(j,2,i)=fac8*(dc_norm(j,i+nres)- & - scala2*dc_norm(j,i))-cosa*fac7*dcostheta(j,2,i+1) - dalpha(j,2,i)=-1/sina*dcosalpha(j,2,i) - dcosalpha(j,3,i)=(fac9*(dc_norm(j,i)- & - dc_norm(j,i-1))-(cosa*dc_norm(j,i+nres))/ & - vbld(i+nres)) - dalpha(j,3,i)=-1/sina*dcosalpha(j,3,i) - enddo -! obtaining the derivatives of omega from sines - if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or. & - omeg(i).gt.pi34.and.omeg(i).le.pi.or. & - omeg(i).gt.-pi.and.omeg(i).le.-pi34) then - fac15=dcos(theta(i+1))/(dsin(theta(i+1))* & - dsin(theta(i+1))) - fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i))) - fac17=1.0d0/(dsin(theta(i+1))*dsin(alph(i))) - call vecpr(dc_norm(1,i+nres),dc_norm(1,i),vo1) - call vecpr(dc_norm(1,i+nres),dc_norm(1,i-1),vo2) - call vecpr(dc_norm(1,i),dc_norm(1,i-1),vo3) - coso_inv=1.0d0/dcos(omeg(i)) + if(itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then + fac5=1.0d0/dsqrt(2*(1+dcos(theta(i+1)))) + fac6=fac5/vbld(i) + fac7=fac5*fac5 + fac8=fac5/vbld(i+1) + fac9=fac5/vbld(i+nres) + scala1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres)) + scala2=scalar(dc_norm(1,i),dc_norm(1,i+nres)) + cosa=dsqrt(0.5d0/(1.0d0+dcos(theta(i+1))))* & + (scalar(dC_norm(1,i),dC_norm(1,i+nres)) & + -scalar(dC_norm(1,i-1),dC_norm(1,i+nres))) + sina=sqrt(1-cosa*cosa) + sino=dsin(omeg(i)) + ! write (iout,*) "i",i," cosa",cosa," sina",sina," sino",sino + do j=1,3 + dcosalpha(j,1,i)=fac6*(scala1*dc_norm(j,i-1)- & + dc_norm(j,i+nres))-cosa*fac7*dcostheta(j,1,i+1) + dalpha(j,1,i)=-1/sina*dcosalpha(j,1,i) + dcosalpha(j,2,i)=fac8*(dc_norm(j,i+nres)- & + scala2*dc_norm(j,i))-cosa*fac7*dcostheta(j,2,i+1) + dalpha(j,2,i)=-1/sina*dcosalpha(j,2,i) + dcosalpha(j,3,i)=(fac9*(dc_norm(j,i)- & + dc_norm(j,i-1))-(cosa*dc_norm(j,i+nres))/ & + vbld(i+nres)) + dalpha(j,3,i)=-1/sina*dcosalpha(j,3,i) + enddo + ! obtaining the derivatives of omega from sines + if(omeg(i).gt.-pi4.and.omeg(i).le.pi4.or. & + omeg(i).gt.pi34.and.omeg(i).le.pi.or. & + omeg(i).gt.-pi.and.omeg(i).le.-pi34) then + fac15=dcos(theta(i+1))/(dsin(theta(i+1))* & + dsin(theta(i+1))) + fac16=dcos(alph(i))/(dsin(alph(i))*dsin(alph(i))) + fac17=1.0d0/(dsin(theta(i+1))*dsin(alph(i))) + call vecpr(dc_norm(1,i+nres),dc_norm(1,i),vo1) + call vecpr(dc_norm(1,i+nres),dc_norm(1,i-1),vo2) + call vecpr(dc_norm(1,i),dc_norm(1,i-1),vo3) + coso_inv=1.0d0/dcos(omeg(i)) + do j=1,3 + dsinomega(j,1,i)=sino*(fac15*dcostheta(j,1,i+1) & + +fac16*dcosalpha(j,1,i))-fac17/vbld(i)*vo1(j)- & + (sino*dc_norm(j,i-1))/vbld(i) + domega(j,1,i)=coso_inv*dsinomega(j,1,i) + dsinomega(j,2,i)=sino*(fac15*dcostheta(j,2,i+1) & + +fac16*dcosalpha(j,2,i))+fac17/vbld(i+1)*vo2(j) & + -sino*dc_norm(j,i)/vbld(i+1) + domega(j,2,i)=coso_inv*dsinomega(j,2,i) + dsinomega(j,3,i)=sino*fac16*dcosalpha(j,3,i)- & + fac17/vbld(i+nres)*vo3(j)-sino*dc_norm(j,i+nres)/ & + vbld(i+nres) + domega(j,3,i)=coso_inv*dsinomega(j,3,i) + enddo + else + ! obtaining the derivatives of omega from cosines + fac10=sqrt(0.5d0*(1-dcos(theta(i+1)))) + fac11=sqrt(0.5d0*(1+dcos(theta(i+1)))) + fac12=fac10*sina + fac13=fac12*fac12 + fac14=sina*sina + do j=1,3 + dcosomega(j,1,i)=(-(0.25d0*cosa/fac11* & + dcostheta(j,1,i+1)+fac11*dcosalpha(j,1,i))*fac12+ & + (0.25d0/fac10*sina*dcostheta(j,1,i+1)+cosa/sina* & + fac10*dcosalpha(j,1,i))*(scala2-fac11*cosa))/fac13 + domega(j,1,i)=-1/sino*dcosomega(j,1,i) + dcosomega(j,2,i)=(((dc_norm(j,i+nres)-scala2* & + dc_norm(j,i))/vbld(i+1)-0.25d0*cosa/fac11* & + dcostheta(j,2,i+1)-fac11*dcosalpha(j,2,i))*fac12+ & + (scala2-fac11*cosa)*(0.25d0*sina/fac10* & + dcostheta(j,2,i+1)+fac10*cosa/sina*dcosalpha(j,2,i)))/fac13 + domega(j,2,i)=-1/sino*dcosomega(j,2,i) + dcosomega(j,3,i)=1/fac10*((1/vbld(i+nres)*(dc_norm(j,i)- & + scala2*dc_norm(j,i+nres))-fac11*dcosalpha(j,3,i))*sina+ & + (scala2-fac11*cosa)*(cosa/sina*dcosalpha(j,3,i)))/fac14 + domega(j,3,i)=-1/sino*dcosomega(j,3,i) + enddo + endif + else do j=1,3 - dsinomega(j,1,i)=sino*(fac15*dcostheta(j,1,i+1) & - +fac16*dcosalpha(j,1,i))-fac17/vbld(i)*vo1(j)- & - (sino*dc_norm(j,i-1))/vbld(i) - domega(j,1,i)=coso_inv*dsinomega(j,1,i) - dsinomega(j,2,i)=sino*(fac15*dcostheta(j,2,i+1) & - +fac16*dcosalpha(j,2,i))+fac17/vbld(i+1)*vo2(j) & - -sino*dc_norm(j,i)/vbld(i+1) - domega(j,2,i)=coso_inv*dsinomega(j,2,i) - dsinomega(j,3,i)=sino*fac16*dcosalpha(j,3,i)- & - fac17/vbld(i+nres)*vo3(j)-sino*dc_norm(j,i+nres)/ & - vbld(i+nres) - domega(j,3,i)=coso_inv*dsinomega(j,3,i) - enddo - else -! obtaining the derivatives of omega from cosines - fac10=sqrt(0.5d0*(1-dcos(theta(i+1)))) - fac11=sqrt(0.5d0*(1+dcos(theta(i+1)))) - fac12=fac10*sina - fac13=fac12*fac12 - fac14=sina*sina - do j=1,3 - dcosomega(j,1,i)=(-(0.25d0*cosa/fac11* & - dcostheta(j,1,i+1)+fac11*dcosalpha(j,1,i))*fac12+ & - (0.25d0/fac10*sina*dcostheta(j,1,i+1)+cosa/sina* & - fac10*dcosalpha(j,1,i))*(scala2-fac11*cosa))/fac13 - domega(j,1,i)=-1/sino*dcosomega(j,1,i) - dcosomega(j,2,i)=(((dc_norm(j,i+nres)-scala2* & - dc_norm(j,i))/vbld(i+1)-0.25d0*cosa/fac11* & - dcostheta(j,2,i+1)-fac11*dcosalpha(j,2,i))*fac12+ & - (scala2-fac11*cosa)*(0.25d0*sina/fac10* & - dcostheta(j,2,i+1)+fac10*cosa/sina*dcosalpha(j,2,i)))/fac13 - domega(j,2,i)=-1/sino*dcosomega(j,2,i) - dcosomega(j,3,i)=1/fac10*((1/vbld(i+nres)*(dc_norm(j,i)- & - scala2*dc_norm(j,i+nres))-fac11*dcosalpha(j,3,i))*sina+ & - (scala2-fac11*cosa)*(cosa/sina*dcosalpha(j,3,i)))/fac14 - domega(j,3,i)=-1/sino*dcosomega(j,3,i) - enddo - endif - else - do j=1,3 - do k=1,3 - dalpha(k,j,i)=0.0d0 - domega(k,j,i)=0.0d0 - enddo - enddo - endif - enddo + do k=1,3 + dalpha(k,j,i)=0.0d0 + domega(k,j,i)=0.0d0 + enddo + enddo + endif + enddo #endif #if defined(MPI) && defined(PARINTDER) - if (nfgtasks.gt.1) then + if (nfgtasks.gt.1) then #ifdef DEBUG -!d write (iout,*) "Gather dtheta" -!d call flush(iout) - write (iout,*) "dtheta before gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2) - enddo + !d write (iout,*) "Gather dtheta" + !d call flush(iout) + write (iout,*) "dtheta before gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),k=1,3),j=1,2) + enddo #endif - call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank),& - MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET,& - king,FG_COMM,IERROR) + call MPI_Gatherv(dtheta(1,1,ithet_start),ithet_count(fg_rank),& + MPI_THET,dtheta(1,1,1),ithet_count(0),ithet_displ(0),MPI_THET,& + king,FG_COMM,IERROR) #ifdef DEBUG -!d write (iout,*) "Gather dphi" -!d call flush(iout) - write (iout,*) "dphi before gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),k=1,3),j=1,3) - enddo + !d write (iout,*) "Gather dphi" + !d call flush(iout) + write (iout,*) "dphi before gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),k=1,3),j=1,3) + enddo #endif - call MPI_Gatherv(dphi(1,1,iphi1_start),iphi1_count(fg_rank),& - MPI_GAM,dphi(1,1,1),iphi1_count(0),iphi1_displ(0),MPI_GAM,& - king,FG_COMM,IERROR) -!d write (iout,*) "Gather dalpha" -!d call flush(iout) + call MPI_Gatherv(dphi(1,1,iphi1_start),iphi1_count(fg_rank),& + MPI_GAM,dphi(1,1,1),iphi1_count(0),iphi1_displ(0),MPI_GAM,& + king,FG_COMM,IERROR) + !d write (iout,*) "Gather dalpha" + !d call flush(iout) #ifdef CRYST_SC - call MPI_Gatherv(dalpha(1,1,ibond_start),ibond_count(fg_rank),& - MPI_GAM,dalpha(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,& - king,FG_COMM,IERROR) -!d write (iout,*) "Gather domega" -!d call flush(iout) - call MPI_Gatherv(domega(1,1,ibond_start),ibond_count(fg_rank),& - MPI_GAM,domega(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,& - king,FG_COMM,IERROR) + call MPI_Gatherv(dalpha(1,1,ibond_start),ibond_count(fg_rank),& + MPI_GAM,dalpha(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,& + king,FG_COMM,IERROR) + !d write (iout,*) "Gather domega" + !d call flush(iout) + call MPI_Gatherv(domega(1,1,ibond_start),ibond_count(fg_rank),& + MPI_GAM,domega(1,1,1),ibond_count(0),ibond_displ(0),MPI_GAM,& + king,FG_COMM,IERROR) #endif - endif + endif #endif #ifdef DEBUG - write (iout,*) "dtheta after gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),j=1,3),k=1,2) - enddo - write (iout,*) "dphi after gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),j=1,3),k=1,3) - enddo - write (iout,*) "dalpha after gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((dalpha(j,k,i),j=1,3),k=1,3) - enddo - write (iout,*) "domega after gather" - do i=1,nres - write (iout,'(i3,3(3f8.5,3x))') i,((domega(j,k,i),j=1,3),k=1,3) - enddo + write (iout,*) "dtheta after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dtheta(j,k,i),j=1,3),k=1,2) + enddo + write (iout,*) "dphi after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dphi(j,k,i),j=1,3),k=1,3) + enddo + write (iout,*) "dalpha after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((dalpha(j,k,i),j=1,3),k=1,3) + enddo + write (iout,*) "domega after gather" + do i=1,nres + write (iout,'(i3,3(3f8.5,3x))') i,((domega(j,k,i),j=1,3),k=1,3) + enddo #endif - return - end subroutine intcartderiv -!----------------------------------------------------------------------------- - subroutine checkintcartgrad -! implicit real*8 (a-h,o-z) -! include 'DIMENSIONS' + return + end subroutine intcartderiv + !----------------------------------------------------------------------------- + subroutine checkintcartgrad + ! implicit real*8 (a-h,o-z) + ! include 'DIMENSIONS' #ifdef MPI - include 'mpif.h' + include 'mpif.h' #endif -! include 'COMMON.CHAIN' -! include 'COMMON.VAR' -! include 'COMMON.GEO' -! include 'COMMON.INTERACT' -! include 'COMMON.DERIV' -! include 'COMMON.IOUNITS' -! include 'COMMON.SETUP' - real(kind=8),dimension(3,2,nres) :: dthetanum !(3,2,maxres) - real(kind=8),dimension(3,3,nres) :: dphinum,dalphanum,domeganum !(3,3,maxres) - real(kind=8),dimension(nres) :: theta_s,phi_s,alph_s,omeg_s !(maxres) - real(kind=8),dimension(3) :: dc_norm_s - real(kind=8) :: aincr=1.0d-5 - integer :: i,j - real(kind=8) :: dcji - do i=1,nres - phi_s(i)=phi(i) - theta_s(i)=theta(i) - alph_s(i)=alph(i) - omeg_s(i)=omeg(i) - enddo -! Check theta gradient - write (iout,*) & - "Analytical (upper) and numerical (lower) gradient of theta" - write (iout,*) - do i=3,nres - do j=1,3 - dcji=dc(j,i-2) - dc(j,i-2)=dcji+aincr - call chainbuild_cart - call int_from_cart1(.false.) + ! include 'COMMON.CHAIN' + ! include 'COMMON.VAR' + ! include 'COMMON.GEO' + ! include 'COMMON.INTERACT' + ! include 'COMMON.DERIV' + ! include 'COMMON.IOUNITS' + ! include 'COMMON.SETUP' + real(kind=8),dimension(3,2,nres) :: dthetanum !(3,2,maxres) + real(kind=8),dimension(3,3,nres) :: dphinum,dalphanum,domeganum !(3,3,maxres) + real(kind=8),dimension(nres) :: theta_s,phi_s,alph_s,omeg_s !(maxres) + real(kind=8),dimension(3) :: dc_norm_s + real(kind=8) :: aincr=1.0d-5 + integer :: i,j + real(kind=8) :: dcji + do i=1,nres + phi_s(i)=phi(i) + theta_s(i)=theta(i) + alph_s(i)=alph(i) + omeg_s(i)=omeg(i) + enddo + ! Check theta gradient + write (iout,*) & + "Analytical (upper) and numerical (lower) gradient of theta" + write (iout,*) + do i=3,nres + do j=1,3 + dcji=dc(j,i-2) + dc(j,i-2)=dcji+aincr + call chainbuild_cart + call int_from_cart1(.false.) dthetanum(j,1,i)=(theta(i)-theta_s(i))/aincr dc(j,i-2)=dcji dcji=dc(j,i-1) dc(j,i-1)=dc(j,i-1)+aincr - call chainbuild_cart + call chainbuild_cart dthetanum(j,2,i)=(theta(i)-theta_s(i))/aincr dc(j,i-1)=dcji enddo @@ -16546,7 +17130,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' dc(j,i-3)=dcji+aincr call chainbuild_cart dphinum(j,1,i)=(phi(i)-phi_s(i))/aincr - dc(j,i-3)=dcji + dc(j,i-3)=dcji dcji=dc(j,i-2) dc(j,i-2)=dcji+aincr call chainbuild_cart @@ -16572,28 +17156,28 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' write (iout,*) & "Analytical (upper) and numerical (lower) gradient of alpha" do i=2,nres-1 - if(itype(i).ne.10) then - do j=1,3 - dcji=dc(j,i-1) - dc(j,i-1)=dcji+aincr + if(itype(i,1).ne.10) then + do j=1,3 + dcji=dc(j,i-1) + dc(j,i-1)=dcji+aincr call chainbuild_cart dalphanum(j,1,i)=(alph(i)-alph_s(i)) & - /aincr - dc(j,i-1)=dcji + /aincr + dc(j,i-1)=dcji dcji=dc(j,i) dc(j,i)=dcji+aincr call chainbuild_cart dalphanum(j,2,i)=(alph(i)-alph_s(i)) & - /aincr + /aincr dc(j,i)=dcji dcji=dc(j,i+nres) dc(j,i+nres)=dc(j,i+nres)+aincr call chainbuild_cart dalphanum(j,3,i)=(alph(i)-alph_s(i)) & - /aincr + /aincr dc(j,i+nres)=dcji enddo - endif + endif !el write (iout,'(i5,3(3f10.5,5x))') i,(dalpha(j,1,i),j=1,3),& !el (dalpha(j,2,i),j=1,3),(dalpha(j,3,i),j=1,3) !el write (iout,'(5x,3(3f10.5,5x))') (dalphanum(j,1,i),j=1,3),& @@ -16608,28 +17192,28 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' write (iout,*) & "Analytical (upper) and numerical (lower) gradient of omega" do i=2,nres-1 - if(itype(i).ne.10) then - do j=1,3 - dcji=dc(j,i-1) - dc(j,i-1)=dcji+aincr + if(itype(i,1).ne.10) then + do j=1,3 + dcji=dc(j,i-1) + dc(j,i-1)=dcji+aincr call chainbuild_cart domeganum(j,1,i)=(omeg(i)-omeg_s(i)) & - /aincr - dc(j,i-1)=dcji + /aincr + dc(j,i-1)=dcji dcji=dc(j,i) dc(j,i)=dcji+aincr call chainbuild_cart domeganum(j,2,i)=(omeg(i)-omeg_s(i)) & - /aincr + /aincr dc(j,i)=dcji dcji=dc(j,i+nres) dc(j,i+nres)=dc(j,i+nres)+aincr call chainbuild_cart domeganum(j,3,i)=(omeg(i)-omeg_s(i)) & - /aincr + /aincr dc(j,i+nres)=dcji enddo - endif + endif !el write (iout,'(i5,3(3f10.5,5x))') i,(domega(j,1,i),j=1,3),& !el (domega(j,2,i),j=1,3),(domega(j,3,i),j=1,3) !el write (iout,'(5x,3(3f10.5,5x))') (domeganum(j,1,i),j=1,3),& @@ -16654,7 +17238,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! include 'COMMON.VAR' integer :: i,j,jl,k,l,il,kl,nl,np,ip,kp,seg1,seg2,seg3,seg4,secseg integer :: kkk,nsep=3 - real(kind=8) :: qm !dist, + real(kind=8) :: qm !dist, real(kind=8) :: qq,qqij,qqijCM,dij,d0ij,dijCM,d0ijCM,qqmax logical :: lprn=.false. logical :: flag @@ -16674,7 +17258,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' (cref(3,jl,kkk)-cref(3,il,kkk))**2) dij=dist(il,jl) qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2) - if (itype(il).ne.10 .or. itype(jl).ne.10) then + if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then nl=nl+1 d0ijCM=dsqrt( & (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ & @@ -16685,7 +17269,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' endif qq = qq+qqij+qqijCM enddo - enddo + enddo qq = qq/nl else do il=seg1,seg2 @@ -16701,7 +17285,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' (cref(3,jl,kkk)-cref(3,il,kkk))**2) dij=dist(il,jl) qqij = dexp(-0.5d0*((dij-d0ij)/(sigm(d0ij)))**2) - if (itype(il).ne.10 .or. itype(jl).ne.10) then + if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then nl=nl+1 d0ijCM=dsqrt( & (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ & @@ -16736,12 +17320,12 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' logical :: lprn=.false. logical :: flag real(kind=8) :: sim,dd0,fac,ddqij -!el sigm(x)=0.25d0*x ! local function +!el sigm(x)=0.25d0*x ! local function do kkk=1,nperm do i=0,nres do j=1,3 dqwol(j,i)=0.0d0 - dxqwol(j,i)=0.0d0 + dxqwol(j,i)=0.0d0 enddo enddo nl=0 @@ -16757,13 +17341,13 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' sim = sim*sim dd0 = dij-d0ij fac = dd0*sim/dij*dexp(-0.5d0*dd0*dd0*sim) - do k=1,3 + do k=1,3 ddqij = (c(k,il)-c(k,jl))*fac dqwol(k,il)=dqwol(k,il)+ddqij dqwol(k,jl)=dqwol(k,jl)-ddqij enddo - - if (itype(il).ne.10 .or. itype(jl).ne.10) then + + if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then nl=nl+1 d0ijCM=dsqrt( & (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ & @@ -16779,9 +17363,9 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' dxqwol(k,il)=dxqwol(k,il)+ddqij dxqwol(k,jl)=dxqwol(k,jl)-ddqij enddo - endif + endif enddo - enddo + enddo else do il=seg1,seg2 if((seg3-il).lt.3) then @@ -16804,7 +17388,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' dqwol(k,il)=dqwol(k,il)+ddqij dqwol(k,jl)=dqwol(k,jl)-ddqij enddo - if (itype(il).ne.10 .or. itype(jl).ne.10) then + if (itype(il,1).ne.10 .or. itype(jl,1).ne.10) then nl=nl+1 d0ijCM=dsqrt( & (cref(1,jl+nres,kkk)-cref(1,il+nres,kkk))**2+ & @@ -16822,7 +17406,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo endif enddo - enddo + enddo endif enddo do i=0,nres @@ -16924,11 +17508,11 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' Ucdfrag=wfrag(i,iset)*harmonicprim(qfrag(i),& qinfrag(i,iset)) ! hm1=harmonic(qfrag(i,iset),qinfrag(i,iset)) -! hm2=harmonic(qfrag(i,iset)+delta,qinfrag(i,iset)) -! hmnum=(hm2-hm1)/delta +! hm2=harmonic(qfrag(i,iset)+delta,qinfrag(i,iset)) +! hmnum=(hm2-hm1)/delta ! write(iout,*) "harmonicprim frag",harmonicprim(qfrag(i,iset), ! & qinfrag(i,iset)) -! write(iout,*) "harmonicnum frag", hmnum +! write(iout,*) "harmonicnum frag", hmnum ! Calculating the derivatives of Q with respect to cartesian coordinates call qwolynes_prim(ifrag(1,i,iset),ifrag(2,i,iset),.true.,& idummy,idummy) @@ -16950,7 +17534,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' dUxconst(j,ii)=dUxconst(j,ii)+ucdfrag*dxqwol(j,ii) enddo enddo - enddo + enddo do i=1,npair kstart=ifrag(1,ipair(1,i,iset),iset) kend=ifrag(2,ipair(1,i,iset),iset) @@ -16961,11 +17545,11 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! Calculating dU/dQ Ucdpair=wpair(i,iset)*harmonicprim(qpair(i),qinpair(i,iset)) ! hm1=harmonic(qpair(i),qinpair(i,iset)) -! hm2=harmonic(qpair(i)+delta,qinpair(i,iset)) -! hmnum=(hm2-hm1)/delta +! hm2=harmonic(qpair(i)+delta,qinpair(i,iset)) +! hmnum=(hm2-hm1)/delta ! write(iout,*) "harmonicprim pair ",harmonicprim(qpair(i), ! & qinpair(i,iset)) -! write(iout,*) "harmonicnum pair ", hmnum +! write(iout,*) "harmonicnum pair ", hmnum ! Calculating dQ/dXi call qwolynes_prim(kstart,kend,.false.,& lstart,lend) @@ -17002,7 +17586,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do j=1,3 dudxconst(j,i)=duxconst(j,i) enddo - enddo + enddo ! write(iout,*) "dU/ddc backbone " ! do ii=0,nres ! write(iout,'(i5,3e15.5)') ii, (dudconst(j,ii),j=1,3) @@ -17051,7 +17635,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' cdummy(j,i)=dc(j,i) dc(j,i)=dc(j,i)+delta call chainbuild_cart - uzap2=0.0d0 + uzap2=0.0d0 do ii=1,nfrag qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,& idummy,idummy) @@ -17085,7 +17669,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),& qinpair(ii,iset)) enddo - ducartan(j,i)=(uzap2-uzap1)/(delta) + ducartan(j,i)=(uzap2-uzap1)/(delta) enddo enddo ! Calculating numerical gradients for dU/ddx @@ -17095,7 +17679,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' cdummy(j,i)=dc(j,i+nres) dc(j,i+nres)=dc(j,i+nres)+delta call chainbuild_cart - uzap2=0.0d0 + uzap2=0.0d0 do ii=1,nfrag qfrag(ii)=qwolynes(ifrag(1,ii,iset),ifrag(2,ii,iset),.true.,& idummy,idummy) @@ -17129,7 +17713,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' uzap1=uzap1+wpair(ii,iset)*harmonic(qpair(ii),& qinpair(ii,iset)) enddo - duxcartan(j,i)=(uzap2-uzap1)/(delta) + duxcartan(j,i)=(uzap2-uzap1)/(delta) enddo enddo write(iout,*) "Numerical dUconst/ddc backbone " @@ -17295,13 +17879,13 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !el allocate(dyn_ssbond_ij(iatsc_s:iatsc_e,nres)) !el allocate(dyn_ssbond_ij(0:nres+4,nres)) - itypi=itype(i) + itypi=itype(i,1) dxi=dc_norm(1,nres+i) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) dsci_inv=vbld_inv(i+nres) - itypj=itype(j) + itypj=itype(j,1) xj=c(1,nres+j)-c(1,nres+i) yj=c(2,nres+j)-c(2,nres+i) zj=c(3,nres+j)-c(3,nres+i) @@ -17612,6 +18196,176 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' return end subroutine dyn_ssbond_ene +!-------------------------------------------------------------------------- + subroutine triple_ssbond_ene(resi,resj,resk,eij) +! implicit none +! Includes + use calc_data + use comm_sschecks +! include 'DIMENSIONS' +! include 'COMMON.SBRIDGE' +! include 'COMMON.CHAIN' +! include 'COMMON.DERIV' +! include 'COMMON.LOCAL' +! include 'COMMON.INTERACT' +! include 'COMMON.VAR' +! include 'COMMON.IOUNITS' +! include 'COMMON.CALC' +#ifndef CLUST +#ifndef WHAM + use MD_data +! include 'COMMON.MD' +! use MD, only: totT,t_bath +#endif +#endif + double precision h_base + external h_base + +!c Input arguments + integer resi,resj,resk,m,itypi,itypj,itypk + +!c Output arguments + double precision eij,eij1,eij2,eij3 + +!c Local variables + logical havebond +!c integer itypi,itypj,k,l + double precision rrij,ssd,deltat1,deltat2,deltat12,cosphi + double precision rrik,rrjk,rik,rjk,xi,xk,yi,yk,zi,zk,xij,yij,zij + double precision xik,yik,zik,xjk,yjk,zjk,dxk,dyk,dzk + double precision sig0ij,ljd,sig,fac,e1,e2 + double precision dcosom1(3),dcosom2(3),ed + double precision pom1,pom2 + double precision ljA,ljB,ljXs + double precision d_ljB(1:3) + double precision ssA,ssB,ssC,ssXs + double precision ssxm,ljxm,ssm,ljm + double precision d_ssxm(1:3),d_ljxm(1:3),d_ssm(1:3),d_ljm(1:3) + eij=0.0 + if (dtriss.eq.0) return + i=resi + j=resj + k=resk +!C write(iout,*) resi,resj,resk + itypi=itype(i,1) + dxi=dc_norm(1,nres+i) + dyi=dc_norm(2,nres+i) + dzi=dc_norm(3,nres+i) + dsci_inv=vbld_inv(i+nres) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + itypj=itype(j,1) + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + + dxj=dc_norm(1,nres+j) + dyj=dc_norm(2,nres+j) + dzj=dc_norm(3,nres+j) + dscj_inv=vbld_inv(j+nres) + itypk=itype(k,1) + xk=c(1,nres+k) + yk=c(2,nres+k) + zk=c(3,nres+k) + + dxk=dc_norm(1,nres+k) + dyk=dc_norm(2,nres+k) + dzk=dc_norm(3,nres+k) + dscj_inv=vbld_inv(k+nres) + xij=xj-xi + xik=xk-xi + xjk=xk-xj + yij=yj-yi + yik=yk-yi + yjk=yk-yj + zij=zj-zi + zik=zk-zi + zjk=zk-zj + rrij=(xij*xij+yij*yij+zij*zij) + rij=dsqrt(rrij) ! sc_angular needs rij to really be the inverse + rrik=(xik*xik+yik*yik+zik*zik) + rik=dsqrt(rrik) + rrjk=(xjk*xjk+yjk*yjk+zjk*zjk) + rjk=dsqrt(rrjk) +!C there are three combination of distances for each trisulfide bonds +!C The first case the ith atom is the center +!C Energy function is E=d/(a*(x-y)**2+b*(x+y)**2+c) where x is first +!C distance y is second distance the a,b,c,d are parameters derived for +!C this problem d parameter was set as a penalty currenlty set to 1. + if ((iabs(j-i).le.2).or.(iabs(i-k).le.2)) then + eij1=0.0d0 + else + eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**6+ctriss) + endif +!C second case jth atom is center + if ((iabs(j-i).le.2).or.(iabs(j-k).le.2)) then + eij2=0.0d0 + else + eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**6+ctriss) + endif +!C the third case kth atom is the center + if ((iabs(i-k).le.2).or.(iabs(j-k).le.2)) then + eij3=0.0d0 + else + eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**6+ctriss) + endif +!C eij2=0.0 +!C eij3=0.0 +!C eij1=0.0 + eij=eij1+eij2+eij3 +!C write(iout,*)i,j,k,eij +!C The energy penalty calculated now time for the gradient part +!C derivative over rij + fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) & + -eij2**2/dtriss*(2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5) + gg(1)=xij*fac/rij + gg(2)=yij*fac/rij + gg(3)=zij*fac/rij + do m=1,3 + gvdwx(m,i)=gvdwx(m,i)-gg(m) + gvdwx(m,j)=gvdwx(m,j)+gg(m) + enddo + + do l=1,3 + gvdwc(l,i)=gvdwc(l,i)-gg(l) + gvdwc(l,j)=gvdwc(l,j)+gg(l) + enddo +!C now derivative over rik + fac=-eij1**2/dtriss* & + (-2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5) & + -eij3**2/dtriss*(2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5) + gg(1)=xik*fac/rik + gg(2)=yik*fac/rik + gg(3)=zik*fac/rik + do m=1,3 + gvdwx(m,i)=gvdwx(m,i)-gg(m) + gvdwx(m,k)=gvdwx(m,k)+gg(m) + enddo + do l=1,3 + gvdwc(l,i)=gvdwc(l,i)-gg(l) + gvdwc(l,k)=gvdwc(l,k)+gg(l) + enddo +!C now derivative over rjk + fac=-eij2**2/dtriss* & + (-2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)- & + eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5) + gg(1)=xjk*fac/rjk + gg(2)=yjk*fac/rjk + gg(3)=zjk*fac/rjk + do m=1,3 + gvdwx(m,j)=gvdwx(m,j)-gg(m) + gvdwx(m,k)=gvdwx(m,k)+gg(m) + enddo + do l=1,3 + gvdwc(l,j)=gvdwc(l,j)-gg(l) + gvdwc(l,k)=gvdwc(l,k)+gg(l) + enddo + return + end subroutine triple_ssbond_ene + + + !----------------------------------------------------------------------------- real(kind=8) function h_base(x,deriv) ! A smooth function going 0->1 in range [0,1] @@ -17758,15 +18512,18 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' diff=newnss-nss !mc write(iout,*)"NEWNSS ",newnss,(newihpb(i),newjhpb(i),i=1,newnss) - +! print *,newnss,nss,maxdim do i=1,nss found=.false. +! print *,newnss do j=1,newnss +!! print *,j if (idssb(i).eq.newihpb(j) .and. & jdssb(i).eq.newjhpb(j)) found=.true. enddo #ifndef CLUST #ifndef WHAM +! write(iout,*) "found",found,i,j if (.not.found.and.fg_rank.eq.0) & write(iout,'(a15,f12.2,f8.1,2i5)') & "SSBOND_BREAK",totT,t_bath,idssb(i),jdssb(i) @@ -17777,11 +18534,13 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' do i=1,newnss found=.false. do j=1,nss +! print *,i,j if (newihpb(i).eq.idssb(j) .and. & newjhpb(i).eq.jdssb(j)) found=.true. enddo #ifndef CLUST #ifndef WHAM +! write(iout,*) "found",found,i,j if (.not.found.and.fg_rank.eq.0) & write(iout,'(a15,f12.2,f8.1,2i5)') & "SSBOND_FORM",totT,t_bath,newihpb(i),newjhpb(i) @@ -17811,10 +18570,10 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' real(kind=8) :: fracinbuf,eliptran,sslip,positi,ssgradlip integer :: i eliptran=0.0 - print *, "I am in eliptran" +! print *, "I am in eliptran" do i=ilip_start,ilip_end !C do i=1,1 - if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1).or.(i.eq.nres))& + if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1).or.(i.eq.nres))& cycle positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize)) @@ -17860,7 +18619,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo ! here starts the side chain transfer do i=ilip_start,ilip_end - if (itype(i).eq.ntyp1) cycle + if (itype(i,1).eq.ntyp1) cycle positi=(mod(c(3,i+nres),boxzsize)) if (positi.le.0) positi=positi+boxzsize !C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop @@ -17876,25 +18635,25 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !C lipbufthick is thickenes of lipid buffore sslip=sscalelip(fracinbuf) ssgradlip=-sscagradlip(fracinbuf)/lipbufthick - eliptran=eliptran+sslip*liptranene(itype(i)) + eliptran=eliptran+sslip*liptranene(itype(i,1)) gliptranx(3,i)=gliptranx(3,i) & - +ssgradlip*liptranene(itype(i)) + +ssgradlip*liptranene(itype(i,1)) gliptranc(3,i-1)= gliptranc(3,i-1) & - +ssgradlip*liptranene(itype(i)) + +ssgradlip*liptranene(itype(i,1)) !C print *,"doing sccale for lower part" elseif (positi.gt.bufliptop) then fracinbuf=1.0d0- & ((bordliptop-positi)/lipbufthick) sslip=sscalelip(fracinbuf) ssgradlip=sscagradlip(fracinbuf)/lipbufthick - eliptran=eliptran+sslip*liptranene(itype(i)) + eliptran=eliptran+sslip*liptranene(itype(i,1)) gliptranx(3,i)=gliptranx(3,i) & - +ssgradlip*liptranene(itype(i)) + +ssgradlip*liptranene(itype(i,1)) gliptranc(3,i-1)= gliptranc(3,i-1) & - +ssgradlip*liptranene(itype(i)) + +ssgradlip*liptranene(itype(i,1)) !C print *, "doing sscalefor top part",sslip,fracinbuf else - eliptran=eliptran+liptranene(itype(i)) + eliptran=eliptran+liptranene(itype(i,1)) !C print *,"I am in true lipid" endif endif ! if in lipid or buffor @@ -17904,86 +18663,732 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo return end subroutine Eliptransfer -!-------------------------------------------------------------------------------- -!C first for shielding is setting of function of side-chains - - subroutine set_shield_fac2 - real(kind=8) :: div77_81=0.974996043d0, & - div4_81=0.2222222222d0 - real (kind=8) :: dist_pep_side,dist_side_calf,dist_pept_group, & - scale_fac_dist,fac_help_scale,VofOverlap,VolumeTotal,costhet,& - short,long,sinthet,costhet_fac,sh_frac_dist,rkprim,cosphi, & - sinphi,cosphi_fac,pep_side0pept_group,cosalfa,fac_alfa_sin -!C the vector between center of side_chain and peptide group - real(kind=8),dimension(3) :: pep_side_long,side_calf, & - pept_group,costhet_grad,cosphi_grad_long, & - cosphi_grad_loc,pep_side_norm,side_calf_norm, & - sh_frac_dist_grad,pep_side - integer i,j,k -!C write(2,*) "ivec",ivec_start,ivec_end - do i=1,nres - fac_shield(i)=0.0d0 +!----------------------------------NANO FUNCTIONS +!C----------------------------------------------------------------------- +!C----------------------------------------------------------- +!C This subroutine is to mimic the histone like structure but as well can be +!C utilizet to nanostructures (infinit) small modification has to be used to +!C make it finite (z gradient at the ends has to be changes as well as the x,y +!C gradient has to be modified at the ends +!C The energy function is Kihara potential +!C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6) +!C 4eps is depth of well sigma is r_minimum r is distance from center of tube +!C and r0 is the excluded size of nanotube (can be set to 0 if we want just a +!C simple Kihara potential + subroutine calctube(Etube) + real(kind=8),dimension(3) :: vectube + real(kind=8) :: Etube,xtemp,xminact,yminact,& + ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi, & + sc_aa_tube,sc_bb_tube + integer :: i,j,iti + Etube=0.0d0 + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +!C first we calculate the distance from tube center +!C for UNRES + do i=itube_start,itube_end +!C lets ommit dummy atoms for now + if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle +!C now calculate distance from center of tube and direction vectors + xmin=boxxsize + ymin=boxysize +! Find minimum distance in periodic box + do j=-1,1 + vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) + +!C as the tube is infinity we do not calculate the Z-vector use of Z +!C as chosen axis + vectube(3)=0.0d0 +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 +!C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6 +!C write(iout,*) "TU13",i,rdiff6,enetube(i) +!C print *,rdiff,rdiff6,pep_aa_tube +!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +!C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- & + 6.0d0*pep_bb_tube)/rdiff6/rdiff +!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +!C &rdiff,fac +!C now direction of gg_tube vector do j=1,3 - grad_shield(j,i)=0.0d0 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 enddo - enddo - do i=ivec_start,ivec_end -!C do i=1,nres-1 -!C if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle - ishield_list(i)=0 - if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle -!Cif there two consequtive dummy atoms there is no peptide group between them -!C the line below has to be changed for FGPROC>1 - VolumeTotal=0.0 - do k=1,nres - if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle - dist_pep_side=0.0 - dist_side_calf=0.0 - do j=1,3 -!C first lets set vector conecting the ithe side-chain with kth side-chain - pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 -!C pep_side(j)=2.0d0 -!C and vector conecting the side-chain with its proper calfa - side_calf(j)=c(j,k+nres)-c(j,k) -!C side_calf(j)=2.0d0 - pept_group(j)=c(j,i)-c(j,i+1) -!C lets have their lenght - dist_pep_side=pep_side(j)**2+dist_pep_side - dist_side_calf=dist_side_calf+side_calf(j)**2 - dist_pept_group=dist_pept_group+pept_group(j)**2 - enddo - dist_pep_side=sqrt(dist_pep_side) - dist_pept_group=sqrt(dist_pept_group) - dist_side_calf=sqrt(dist_side_calf) - do j=1,3 - pep_side_norm(j)=pep_side(j)/dist_pep_side - side_calf_norm(j)=dist_side_calf - enddo -!C now sscale fraction - sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield -!C print *,buff_shield,"buff" -!C now sscale - if (sh_frac_dist.le.0.0) cycle -!C print *,ishield_list(i),i -!C If we reach here it means that this side chain reaches the shielding sphere -!C Lets add him to the list for gradient - ishield_list(i)=ishield_list(i)+1 -!C ishield_list is a list of non 0 side-chain that contribute to factor gradient -!C this list is essential otherwise problem would be O3 - shield_list(ishield_list(i),i)=k -!C Lets have the sscale value - if (sh_frac_dist.gt.1.0) then - scale_fac_dist=1.0d0 - do j=1,3 - sh_frac_dist_grad(j)=0.0d0 + enddo +!C basically thats all code now we split for side-chains (REMEMBER to sum up at the END) +!C print *,gg_tube(1,0),"TU" + + + do i=itube_start,itube_end +!C Lets not jump over memory as we use many times iti + iti=itype(i,1) +!C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) & +!C in UNRES uncomment the line below as GLY has no side-chain... +!C .or.(iti.eq.10) + ) cycle + xmin=boxxsize + ymin=boxysize + do j=-1,1 + vectube(1)=mod((c(1,i+nres)),boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i+nres)),boxysize) + vectube(2)=vectube(2)+boxysize*j + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif enddo - else - scale_fac_dist=-sh_frac_dist*sh_frac_dist & - *(2.0d0*sh_frac_dist-3.0d0) - fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) & - /dist_pep_side/buff_shield*0.5d0 + vectube(1)=xtemp + vectube(2)=ytemp +!C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2), +!C & tubecenter(2) + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +!C as the tube is infinity we do not calculate the Z-vector use of Z +!C as chosen axis + vectube(3)=0.0d0 +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 +!C for vectorization reasons we will sumup at the end to avoid depenence of previous + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6 + fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- & + 6.0d0*sc_bb_tube/rdiff6/rdiff +!C now direction of gg_tube vector do j=1,3 - sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + enddo + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres) + enddo +!C print *,"ETUBE", etube + return + end subroutine calctube +!C TO DO 1) add to total energy +!C 2) add to gradient summation +!C 3) add reading parameters (AND of course oppening of PARAM file) +!C 4) add reading the center of tube +!C 5) add COMMONs +!C 6) add to zerograd +!C 7) allocate matrices + + +!C----------------------------------------------------------------------- +!C----------------------------------------------------------- +!C This subroutine is to mimic the histone like structure but as well can be +!C utilizet to nanostructures (infinit) small modification has to be used to +!C make it finite (z gradient at the ends has to be changes as well as the x,y +!C gradient has to be modified at the ends +!C The energy function is Kihara potential +!C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6) +!C 4eps is depth of well sigma is r_minimum r is distance from center of tube +!C and r0 is the excluded size of nanotube (can be set to 0 if we want just a +!C simple Kihara potential + subroutine calctube2(Etube) + real(kind=8),dimension(3) :: vectube + real(kind=8) :: Etube,xtemp,xminact,yminact,& + ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi,fracinbuf,& + sstube,ssgradtube,sc_aa_tube,sc_bb_tube + integer:: i,j,iti + Etube=0.0d0 + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +!C first we calculate the distance from tube center +!C first sugare-phosphate group for NARES this would be peptide group +!C for UNRES + do i=itube_start,itube_end +!C lets ommit dummy atoms for now + + if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle +!C now calculate distance from center of tube and direction vectors +!C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) +!C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize +!C vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) +!C if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize + xmin=boxxsize + ymin=boxysize + do j=-1,1 + vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + +!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) + +!C as the tube is infinity we do not calculate the Z-vector use of Z +!C as chosen axis + vectube(3)=0.0d0 +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 +!C THIS FRAGMENT MAKES TUBE FINITE + positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize) + if (positi.le.0) positi=positi+boxzsize +!C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop +!c for each residue check if it is in lipid or lipid water border area +!C respos=mod(c(3,i+nres),boxzsize) +!C print *,positi,bordtubebot,buftubebot,bordtubetop + if ((positi.gt.bordtubebot) & + .and.(positi.lt.bordtubetop)) then +!C the energy transfer exist + if (positi.lt.buftubebot) then + fracinbuf=1.0d0- & + ((positi-bordtubebot)/tubebufthick) +!C lipbufthick is thickenes of lipid buffore + sstube=sscalelip(fracinbuf) + ssgradtube=-sscagradlip(fracinbuf)/tubebufthick +!C print *,ssgradtube, sstube,tubetranene(itype(i,1)) + enetube(i)=enetube(i)+sstube*tubetranenepep +!C gg_tube_SC(3,i)=gg_tube_SC(3,i) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C gg_tube(3,i-1)= gg_tube(3,i-1) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C print *,"doing sccale for lower part" + elseif (positi.gt.buftubetop) then + fracinbuf=1.0d0- & + ((bordtubetop-positi)/tubebufthick) + sstube=sscalelip(fracinbuf) + ssgradtube=sscagradlip(fracinbuf)/tubebufthick + enetube(i)=enetube(i)+sstube*tubetranenepep +!C gg_tube_SC(3,i)=gg_tube_SC(3,i) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C gg_tube(3,i-1)= gg_tube(3,i-1) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C print *, "doing sscalefor top part",sslip,fracinbuf + else + sstube=1.0d0 + ssgradtube=0.0d0 + enetube(i)=enetube(i)+sstube*tubetranenepep +!C print *,"I am in true lipid" + endif + else +!C sstube=0.0d0 +!C ssgradtube=0.0d0 + cycle + endif ! if in lipid or buffor + +!C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=enetube(i)+sstube* & + (pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6) +!C write(iout,*) "TU13",i,rdiff6,enetube(i) +!C print *,rdiff,rdiff6,pep_aa_tube +!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +!C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- & + 6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube +!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +!C &rdiff,fac + +!C now direction of gg_tube vector + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 + enddo + gg_tube(3,i)=gg_tube(3,i) & + +ssgradtube*enetube(i)/sstube/2.0d0 + gg_tube(3,i-1)= gg_tube(3,i-1) & + +ssgradtube*enetube(i)/sstube/2.0d0 + + enddo +!C basically thats all code now we split for side-chains (REMEMBER to sum up at the END) +!C print *,gg_tube(1,0),"TU" + do i=itube_start,itube_end +!C Lets not jump over memory as we use many times iti + iti=itype(i,1) +!C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) & +!!C in UNRES uncomment the line below as GLY has no side-chain... + .or.(iti.eq.10) & + ) cycle + vectube(1)=c(1,i+nres) + vectube(1)=mod(vectube(1),boxxsize) + if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize + vectube(2)=c(2,i+nres) + vectube(2)=mod(vectube(2),boxysize) + if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize + + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) +!C THIS FRAGMENT MAKES TUBE FINITE + positi=(mod(c(3,i+nres),boxzsize)) + if (positi.le.0) positi=positi+boxzsize +!C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop +!c for each residue check if it is in lipid or lipid water border area +!C respos=mod(c(3,i+nres),boxzsize) +!C print *,positi,bordtubebot,buftubebot,bordtubetop + + if ((positi.gt.bordtubebot) & + .and.(positi.lt.bordtubetop)) then +!C the energy transfer exist + if (positi.lt.buftubebot) then + fracinbuf=1.0d0- & + ((positi-bordtubebot)/tubebufthick) +!C lipbufthick is thickenes of lipid buffore + sstube=sscalelip(fracinbuf) + ssgradtube=-sscagradlip(fracinbuf)/tubebufthick +!C print *,ssgradtube, sstube,tubetranene(itype(i,1)) + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1)) +!C gg_tube_SC(3,i)=gg_tube_SC(3,i) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C gg_tube(3,i-1)= gg_tube(3,i-1) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C print *,"doing sccale for lower part" + elseif (positi.gt.buftubetop) then + fracinbuf=1.0d0- & + ((bordtubetop-positi)/tubebufthick) + + sstube=sscalelip(fracinbuf) + ssgradtube=sscagradlip(fracinbuf)/tubebufthick + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1)) +!C gg_tube_SC(3,i)=gg_tube_SC(3,i) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C gg_tube(3,i-1)= gg_tube(3,i-1) +!C &+ssgradtube*tubetranene(itype(i,1)) +!C print *, "doing sscalefor top part",sslip,fracinbuf + else + sstube=1.0d0 + ssgradtube=0.0d0 + enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i,1)) +!C print *,"I am in true lipid" + endif + else +!C sstube=0.0d0 +!C ssgradtube=0.0d0 + cycle + endif ! if in lipid or buffor +!CEND OF FINITE FRAGMENT +!C as the tube is infinity we do not calculate the Z-vector use of Z +!C as chosen axis + vectube(3)=0.0d0 +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 +!C for vectorization reasons we will sumup at the end to avoid depenence of previous + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)& + *sstube+enetube(i+nres) +!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +!C now we calculate gradient + fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-& + 6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube +!C now direction of gg_tube vector + do j=1,3 + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + gg_tube_SC(3,i)=gg_tube_SC(3,i) & + +ssgradtube*enetube(i+nres)/sstube + gg_tube(3,i-1)= gg_tube(3,i-1) & + +ssgradtube*enetube(i+nres)/sstube + + enddo + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres) + enddo +!C print *,"ETUBE", etube + return + end subroutine calctube2 +!===================================================================================================================================== + subroutine calcnano(Etube) + real(kind=8),dimension(3) :: vectube + + real(kind=8) :: Etube,xtemp,xminact,yminact,& + ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,denominator,faccav,& + sc_aa_tube,sc_bb_tube,zmin,ztemp,zminact + integer:: i,j,iti,r + + Etube=0.0d0 +! print *,itube_start,itube_end,"poczatek" + do i=itube_start,itube_end + enetube(i)=0.0d0 + enetube(i+nres)=0.0d0 + enddo +!C first we calculate the distance from tube center +!C first sugare-phosphate group for NARES this would be peptide group +!C for UNRES + do i=itube_start,itube_end +!C lets ommit dummy atoms for now + if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle +!C now calculate distance from center of tube and direction vectors + xmin=boxxsize + ymin=boxysize + zmin=boxzsize + + do j=-1,1 + vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize) + vectube(2)=vectube(2)+boxysize*j + vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=dabs(vectube(1)-tubecenter(1)) + yminact=dabs(vectube(2)-tubecenter(2)) + zminact=dabs(vectube(3)-tubecenter(3)) + + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + if (zmin.gt.zminact) then + zmin=zminact + ztemp=vectube(3) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(3)=ztemp + + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + vectube(3)=vectube(3)-tubecenter(3) + +!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1) +!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2) +!C as the tube is infinity we do not calculate the Z-vector use of Z +!C as chosen axis +!C vectube(3)=0.0d0 +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + vectube(3)=vectube(3)/tub_r +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 +!C for vectorization reasons we will sumup at the end to avoid depenence of previous + enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6 +!C write(iout,*) "TU13",i,rdiff6,enetube(i) +!C print *,rdiff,rdiff6,pep_aa_tube +!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +!C now we calculate gradient + fac=(-12.0d0*pep_aa_tube/rdiff6- & + 6.0d0*pep_bb_tube)/rdiff6/rdiff +!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i), +!C &rdiff,fac + if (acavtubpep.eq.0.0d0) then +!C go to 667 + enecavtube(i)=0.0 + faccav=0.0 + else + denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6) + enecavtube(i)= & + (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep) & + /denominator + enecavtube(i)=0.0 + faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff)) & + *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff) & + +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0) & + /denominator**2.0d0 +!C faccav=0.0 +!C fac=fac+faccav +!C 667 continue + endif + if (energy_dec) write(iout,*),i,rdiff,enetube(i),enecavtube(i) + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0 + gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0 + enddo + enddo + + do i=itube_start,itube_end + enecavtube(i)=0.0d0 +!C Lets not jump over memory as we use many times iti + iti=itype(i,1) +!C lets ommit dummy atoms for now + if ((iti.eq.ntyp1) & +!C in UNRES uncomment the line below as GLY has no side-chain... +!C .or.(iti.eq.10) + ) cycle + xmin=boxxsize + ymin=boxysize + zmin=boxzsize + do j=-1,1 + vectube(1)=dmod((c(1,i+nres)),boxxsize) + vectube(1)=vectube(1)+boxxsize*j + vectube(2)=dmod((c(2,i+nres)),boxysize) + vectube(2)=vectube(2)+boxysize*j + vectube(3)=dmod((c(3,i+nres)),boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=dabs(vectube(1)-tubecenter(1)) + yminact=dabs(vectube(2)-tubecenter(2)) + zminact=dabs(vectube(3)-tubecenter(3)) + + if (xmin.gt.xminact) then + xmin=xminact + xtemp=vectube(1) + endif + if (ymin.gt.yminact) then + ymin=yminact + ytemp=vectube(2) + endif + if (zmin.gt.zminact) then + zmin=zminact + ztemp=vectube(3) + endif + enddo + vectube(1)=xtemp + vectube(2)=ytemp + vectube(3)=ztemp + +!C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2), +!C & tubecenter(2) + vectube(1)=vectube(1)-tubecenter(1) + vectube(2)=vectube(2)-tubecenter(2) + vectube(3)=vectube(3)-tubecenter(3) +!C now calculte the distance + tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2) +!C now normalize vector + vectube(1)=vectube(1)/tub_r + vectube(2)=vectube(2)/tub_r + vectube(3)=vectube(3)/tub_r + +!C calculte rdiffrence between r and r0 + rdiff=tub_r-tubeR0 +!C and its 6 power + rdiff6=rdiff**6.0d0 + sc_aa_tube=sc_aa_tube_par(iti) + sc_bb_tube=sc_bb_tube_par(iti) + enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6 +!C enetube(i+nres)=0.0d0 +!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6 +!C now we calculate gradient + fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- & + 6.0d0*sc_bb_tube/rdiff6/rdiff +!C fac=0.0 +!C now direction of gg_tube vector +!C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12) + if (acavtub(iti).eq.0.0d0) then +!C go to 667 + enecavtube(i+nres)=0.0d0 + faccav=0.0d0 + else + denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6) + enecavtube(i+nres)= & + (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti)) & + /denominator +!C enecavtube(i)=0.0 + faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff)) & + *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff) & + +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0) & + /denominator**2.0d0 +!C faccav=0.0 + fac=fac+faccav +!C 667 continue + endif +!C print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator, +!C & enecavtube(i),faccav +!C print *,"licz=", +!C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) +!C print *,"finene=",enetube(i+nres)+enecavtube(i) + do j=1,3 + gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + if (energy_dec) write(iout,*),i,rdiff,enetube(i+nres),enecavtube(i+nres) + enddo + + + + do i=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) & + +enecavtube(i+nres) + enddo +! do i=1,20 +! print *,"begin", i,"a" +! do r=1,10000 +! rdiff=r/100.0d0 +! rdiff6=rdiff**6.0d0 +! sc_aa_tube=sc_aa_tube_par(i) +! sc_bb_tube=sc_bb_tube_par(i) +! enetube(i)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6 +! denominator=(1.0d0+dcavtub(i)*rdiff6*rdiff6) +! enecavtube(i)= & +! (bcavtub(i)*rdiff+acavtub(i)*dsqrt(rdiff)+ccavtub(i)) & +! /denominator + +! print '(5(f10.3,1x))',rdiff,enetube(i),enecavtube(i),enecavtube(i)+enetube(i) +! enddo +! print *,"end",i,"a" +! enddo +!C print *,"ETUBE", etube + return + end subroutine calcnano + +!=============================================== +!-------------------------------------------------------------------------------- +!C first for shielding is setting of function of side-chains + + subroutine set_shield_fac2 + real(kind=8) :: div77_81=0.974996043d0, & + div4_81=0.2222222222d0 + real (kind=8) :: dist_pep_side,dist_side_calf,dist_pept_group, & + scale_fac_dist,fac_help_scale,VofOverlap,VolumeTotal,costhet,& + short,long,sinthet,costhet_fac,sh_frac_dist,rkprim,cosphi, & + sinphi,cosphi_fac,pep_side0pept_group,cosalfa,fac_alfa_sin +!C the vector between center of side_chain and peptide group + real(kind=8),dimension(3) :: pep_side_long,side_calf, & + pept_group,costhet_grad,cosphi_grad_long, & + cosphi_grad_loc,pep_side_norm,side_calf_norm, & + sh_frac_dist_grad,pep_side + integer i,j,k +!C write(2,*) "ivec",ivec_start,ivec_end + do i=1,nres + fac_shield(i)=0.0d0 + do j=1,3 + grad_shield(j,i)=0.0d0 + enddo + enddo + do i=ivec_start,ivec_end +!C do i=1,nres-1 +!C if ((itype(i,1).eq.ntyp1).and.itype(i+1,1).eq.ntyp1) cycle + ishield_list(i)=0 + if ((itype(i,1).eq.ntyp1).and.itype(i+1,1).eq.ntyp1) cycle +!Cif there two consequtive dummy atoms there is no peptide group between them +!C the line below has to be changed for FGPROC>1 + VolumeTotal=0.0 + do k=1,nres + if ((itype(k,1).eq.ntyp1).or.(itype(k,1).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +!C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +!C pep_side(j)=2.0d0 +!C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +!C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +!C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=sqrt(dist_pep_side) + dist_pept_group=sqrt(dist_pept_group) + dist_side_calf=sqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +!C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +!C print *,buff_shield,"buff" +!C now sscale + if (sh_frac_dist.le.0.0) cycle +!C print *,ishield_list(i),i +!C If we reach here it means that this side chain reaches the shielding sphere +!C Lets add him to the list for gradient + ishield_list(i)=ishield_list(i)+1 +!C ishield_list is a list of non 0 side-chain that contribute to factor gradient +!C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +!C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist & + *(2.0d0*sh_frac_dist-3.0d0) + fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) & + /dist_pep_side/buff_shield*0.5d0 + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) !C sh_frac_dist_grad(j)=0.0d0 !C scale_fac_dist=1.0d0 !C print *,"jestem",scale_fac_dist,fac_help_scale, @@ -17991,8 +19396,8 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo endif !C this is what is now we have the distance scaling now volume... - short=short_r_sidechain(itype(k)) - long=long_r_sidechain(itype(k)) + short=short_r_sidechain(itype(k,1)) + long=long_r_sidechain(itype(k,1)) costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2) sinthet=short/dist_pep_side*costhet !C now costhet_grad @@ -18078,10 +19483,66 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' enddo fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield) -!C write(2,*) "TOTAL VOLUME",i,itype(i),fac_shield(i) +!C write(2,*) "TOTAL VOLUME",i,itype(i,1),fac_shield(i) enddo return end subroutine set_shield_fac2 +!---------------------------------------------------------------------------- +! SOUBROUTINE FOR AFM + subroutine AFMvel(Eafmforce) + use MD_data, only:totTafm + real(kind=8),dimension(3) :: diffafm + real(kind=8) :: afmdist,Eafmforce + integer :: i +!C Only for check grad COMMENT if not used for checkgrad +!C totT=3.0d0 +!C-------------------------------------------------------- +!C print *,"wchodze" + afmdist=0.0d0 + Eafmforce=0.0d0 + do i=1,3 + diffafm(i)=c(i,afmend)-c(i,afmbeg) + afmdist=afmdist+diffafm(i)**2 + enddo + afmdist=dsqrt(afmdist) +! totTafm=3.0 + Eafmforce=0.5d0*forceAFMconst & + *(distafminit+totTafm*velAFMconst-afmdist)**2 +!C Eafmforce=-forceAFMconst*(dist-distafminit) + do i=1,3 + gradafm(i,afmend-1)=-forceAFMconst* & + (distafminit+totTafm*velAFMconst-afmdist) & + *diffafm(i)/afmdist + gradafm(i,afmbeg-1)=forceAFMconst* & + (distafminit+totTafm*velAFMconst-afmdist) & + *diffafm(i)/afmdist + enddo +! print *,'AFM',Eafmforce,totTafm*velAFMconst,afmdist + return + end subroutine AFMvel +!--------------------------------------------------------- + subroutine AFMforce(Eafmforce) + + real(kind=8),dimension(3) :: diffafm +! real(kind=8) ::afmdist + real(kind=8) :: afmdist,Eafmforce + integer :: i + afmdist=0.0d0 + Eafmforce=0.0d0 + do i=1,3 + diffafm(i)=c(i,afmend)-c(i,afmbeg) + afmdist=afmdist+diffafm(i)**2 + enddo + afmdist=dsqrt(afmdist) +! print *,afmdist,distafminit + Eafmforce=-forceAFMconst*(afmdist-distafminit) + do i=1,3 + gradafm(i,afmend-1)=-forceAFMconst*diffafm(i)/afmdist + gradafm(i,afmbeg-1)=forceAFMconst*diffafm(i)/afmdist + enddo +!C print *,'AFM',Eafmforce + return + end subroutine AFMforce !----------------------------------------------------------------------------- #ifdef WHAM @@ -18132,12 +19593,12 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' if(nres.lt.100) then maxconts=nres elseif(nres.lt.200) then - maxconts=0.8*nres ! Max. number of contacts per residue + maxconts=0.8*nres ! Max. number of contacts per residue else maxconts=0.6*nres ! (maxconts=maxres/4) endif - maxcont=12*nres ! Max. number of SC contacts - maxvar=6*nres ! Max. number of variables + maxcont=12*nres ! Max. number of SC contacts + maxvar=6*nres ! Max. number of variables !el maxdim=(nres-1)*(nres-2)/2 ! Max. number of derivatives of virtual-bond maxdim=nres*(nres-2)/2 ! Max. number of derivatives of virtual-bond !---------------------- @@ -18160,6 +19621,19 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' allocate(ielstart_vdw(nres)) allocate(ielend_vdw(nres)) !(maxres) + allocate(nint_gr_nucl(nres)) + allocate(nscp_gr_nucl(nres)) + allocate(ielstart_nucl(nres)) + allocate(ielend_nucl(nres)) +!(maxres) + allocate(istart_nucl(nres,maxint_gr)) + allocate(iend_nucl(nres,maxint_gr)) +!(maxres,maxint_gr) + allocate(iscpstart_nucl(nres,maxint_gr)) + allocate(iscpend_nucl(nres,maxint_gr)) +!(maxres,maxint_gr) + allocate(ielstart_vdw_nucl(nres)) + allocate(ielend_vdw_nucl(nres)) allocate(lentyp(0:nfgtasks-1)) !(0:maxprocs-1) @@ -18327,6 +19801,28 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' allocate(gshieldc_ll(3,-1:nres)) allocate(gshieldc_loc_ll(3,-1:nres)) allocate(grad_shield(3,-1:nres)) + allocate(gg_tube_sc(3,-1:nres)) + allocate(gg_tube(3,-1:nres)) + allocate(gradafm(3,-1:nres)) + allocate(gradb_nucl(3,-1:nres)) + allocate(gradbx_nucl(3,-1:nres)) + allocate(gvdwpsb1(3,-1:nres)) + allocate(gelpp(3,-1:nres)) + allocate(gvdwpsb(3,-1:nres)) + allocate(gelsbc(3,-1:nres)) + allocate(gelsbx(3,-1:nres)) + allocate(gvdwsbx(3,-1:nres)) + allocate(gvdwsbc(3,-1:nres)) + allocate(gsbloc(3,-1:nres)) + allocate(gsblocx(3,-1:nres)) + allocate(gradcorr_nucl(3,-1:nres)) + allocate(gradxorr_nucl(3,-1:nres)) + allocate(gradcorr3_nucl(3,-1:nres)) + allocate(gradxorr3_nucl(3,-1:nres)) + allocate(gvdwpp_nucl(3,-1:nres)) + allocate(gradpepcat(3,-1:nres)) + allocate(gradpepcatx(3,-1:nres)) + allocate(gradcatcat(3,-1:nres)) !(3,maxres) allocate(grad_shield_side(3,50,nres)) allocate(grad_shield_loc(3,50,nres)) @@ -18355,6 +19851,14 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !(3,maxres) allocate(gsccor_loc(-1:nres)) !(maxres) + allocate(gvdwx_scbase(3,-1:nres)) + allocate(gvdwc_scbase(3,-1:nres)) + allocate(gvdwx_pepbase(3,-1:nres)) + allocate(gvdwc_pepbase(3,-1:nres)) + allocate(gvdwx_scpho(3,-1:nres)) + allocate(gvdwc_scpho(3,-1:nres)) + allocate(gvdwc_peppho(3,-1:nres)) + allocate(dtheta(3,2,-1:nres)) !(3,2,maxres) allocate(gscloc(3,-1:nres)) @@ -18432,7 +19936,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' !---------------------- ! common.sbridge ! common /sbridge/ in io_common: read_bridge -!el allocate((:),allocatable :: iss !(maxss) +!el allocate((:),allocatable :: iss !(maxss) ! common /links/ in io_common: read_bridge !el real(kind=8),dimension(:),allocatable :: dhpb,forcon,dhpb1 !(maxdim) !el dhpb1 !!! nie używane !el integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane @@ -18446,14 +19950,18 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! enddo ! enddo - if (nss.gt.0) then - allocate(idssb(nss),jdssb(nss)) +! if (nss.gt.0) then + allocate(idssb(maxdim),jdssb(maxdim)) +! allocate(newihpb(nss),newjhpb(nss)) !(maxdim) - endif +! endif allocate(ishield_list(nres)) allocate(shield_list(50,nres)) allocate(dyn_ss_mask(nres)) allocate(fac_shield(nres)) + allocate(enetube(nres*2)) + allocate(enecavtube(nres*2)) + !(maxres) dyn_ss_mask(:)=.false. !---------------------- @@ -18469,7 +19977,7 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' ! allocate(nlor_sccor(-ntyp:ntyp,-ntyp:ntyp)) !(-ntyp:ntyp,-ntyp:ntyp) ! allocate(vlor1sccor(maxterm_sccor,20,20)) ! allocate(vlor2sccor(maxterm_sccor,20,20)) -! allocate(vlor3sccor(maxterm_sccor,20,20)) !(maxterm_sccor,20,20) +! allocate(vlor3sccor(maxterm_sccor,20,20)) !(maxterm_sccor,20,20) !---------------- allocate(gloc_sc(3,0:2*nres,0:10)) !(3,0:maxres2,10)maxres2=2*maxres @@ -18500,6 +20008,4053 @@ write(iout,*) 'Calling CHECK_ECARTIN else.' return end subroutine alloc_ener_arrays +!----------------------------------------------------------------- + subroutine ebond_nucl(estr_nucl) +!c +!c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds +!c + + real(kind=8),dimension(3) :: u,ud + real(kind=8) :: usum,uprod,uprod1,uprod2,usumsqder + real(kind=8) :: estr_nucl,diff + integer :: iti,i,j,k,nbi + estr_nucl=0.0d0 +!C print *,"I enter ebond" + if (energy_dec) & + write (iout,*) "ibondp_start,ibondp_end",& + ibondp_nucl_start,ibondp_nucl_end + do i=ibondp_nucl_start,ibondp_nucl_end + if (itype(i-1,2).eq.ntyp1_molec(2) .or. & + itype(i,2).eq.ntyp1_molec(2)) cycle +! estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax) +! do j=1,3 +! gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax) +! & *dc(j,i-1)/vbld(i) +! enddo +! if (energy_dec) write(iout,*) +! & "estr1",i,vbld(i),distchainmax, +! & gnmr1(vbld(i),-1.0d0,distchainmax) + + diff = vbld(i)-vbldp0_nucl + if(energy_dec)write(iout,*) "estr_nucl_bb" , i,vbld(i),& + vbldp0_nucl,diff,AKP_nucl*diff*diff + estr_nucl=estr_nucl+diff*diff +! print *,estr_nucl + do j=1,3 + gradb_nucl(j,i-1)=AKP_nucl*diff*dc(j,i-1)/vbld(i) + enddo +!c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3) + enddo + estr_nucl=0.5d0*AKP_nucl*estr_nucl +! print *,"partial sum", estr_nucl,AKP_nucl + + if (energy_dec) & + write (iout,*) "ibondp_start,ibondp_end",& + ibond_nucl_start,ibond_nucl_end + + do i=ibond_nucl_start,ibond_nucl_end +!C print *, "I am stuck",i + iti=itype(i,2) + if (iti.eq.ntyp1_molec(2)) cycle + nbi=nbondterm_nucl(iti) +!C print *,iti,nbi + if (nbi.eq.1) then + diff=vbld(i+nres)-vbldsc0_nucl(1,iti) + + if (energy_dec) & + write (iout,*) "estr_nucl_sc", i,iti,vbld(i+nres),vbldsc0_nucl(1,iti),diff, & + AKSC_nucl(1,iti),AKSC_nucl(1,iti)*diff*diff + estr_nucl=estr_nucl+0.5d0*AKSC_nucl(1,iti)*diff*diff +! print *,estr_nucl + do j=1,3 + gradbx_nucl(j,i)=AKSC_nucl(1,iti)*diff*dc(j,i+nres)/vbld(i+nres) + enddo + else + do j=1,nbi + diff=vbld(i+nres)-vbldsc0_nucl(j,iti) + ud(j)=aksc_nucl(j,iti)*diff + u(j)=abond0_nucl(j,iti)+0.5d0*ud(j)*diff + enddo + uprod=u(1) + do j=2,nbi + uprod=uprod*u(j) + enddo + usum=0.0d0 + usumsqder=0.0d0 + do j=1,nbi + uprod1=1.0d0 + uprod2=1.0d0 + do k=1,nbi + if (k.ne.j) then + uprod1=uprod1*u(k) + uprod2=uprod2*u(k)*u(k) + endif + enddo + usum=usum+uprod1 + usumsqder=usumsqder+ud(j)*uprod2 + enddo + estr_nucl=estr_nucl+uprod/usum + do j=1,3 + gradbx_nucl(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres) + enddo + endif + enddo +!C print *,"I am about to leave ebond" + return + end subroutine ebond_nucl + !----------------------------------------------------------------------------- -!----------------------------------------------------------------------------- + subroutine ebend_nucl(etheta_nucl) + real(kind=8),dimension(nntheterm_nucl+1) :: coskt,sinkt !mmaxtheterm + real(kind=8),dimension(nsingle_nucl+1) :: cosph1,sinph1,cosph2,sinph2 !maxsingle + real(kind=8),dimension(ndouble_nucl+1,ndouble_nucl+1) :: cosph1ph2,sinph1ph2 !maxdouble,maxdouble + logical :: lprn=.false., lprn1=.false. +!el local variables + integer :: i,k,iblock,ityp1,ityp2,ityp3,l,m + real(kind=8) :: dethetai,dephii,dephii1,theti2,phii,phii1,ethetai + real(kind=8) :: aux,etheta_nucl,ccl,ssl,scl,csl,ethetacnstr +! local variables for constrains + real(kind=8) :: difi,thetiii + integer itheta + etheta_nucl=0.0D0 +! print *,"ithet_start",ithet_nucl_start," ithet_end",ithet_nucl_end,nres + do i=ithet_nucl_start,ithet_nucl_end + if ((itype(i-1,2).eq.ntyp1_molec(2)).or.& + (itype(i-2,2).eq.ntyp1_molec(2)).or. & + (itype(i,2).eq.ntyp1_molec(2))) cycle + dethetai=0.0d0 + dephii=0.0d0 + dephii1=0.0d0 + theti2=0.5d0*theta(i) + ityp2=ithetyp_nucl(itype(i-1,2)) + do k=1,nntheterm_nucl + coskt(k)=dcos(k*theti2) + sinkt(k)=dsin(k*theti2) + enddo + if (i.gt.3 .and. itype(i-2,2).ne.ntyp1_molec(2)) then +#ifdef OSF + phii=phi(i) + if (phii.ne.phii) phii=150.0 +#else + phii=phi(i) +#endif + ityp1=ithetyp_nucl(itype(i-2,2)) + do k=1,nsingle_nucl + cosph1(k)=dcos(k*phii) + sinph1(k)=dsin(k*phii) + enddo + else + phii=0.0d0 + ityp1=nthetyp_nucl+1 + do k=1,nsingle_nucl + cosph1(k)=0.0d0 + sinph1(k)=0.0d0 + enddo + endif + + if (i.lt.nres .and. itype(i,2).ne.ntyp1_molec(2)) then +#ifdef OSF + phii1=phi(i+1) + if (phii1.ne.phii1) phii1=150.0 + phii1=pinorm(phii1) +#else + phii1=phi(i+1) +#endif + ityp3=ithetyp_nucl(itype(i,2)) + do k=1,nsingle_nucl + cosph2(k)=dcos(k*phii1) + sinph2(k)=dsin(k*phii1) + enddo + else + phii1=0.0d0 + ityp3=nthetyp_nucl+1 + do k=1,nsingle_nucl + cosph2(k)=0.0d0 + sinph2(k)=0.0d0 + enddo + endif + ethetai=aa0thet_nucl(ityp1,ityp2,ityp3) + do k=1,ndouble_nucl + do l=1,k-1 + ccl=cosph1(l)*cosph2(k-l) + ssl=sinph1(l)*sinph2(k-l) + scl=sinph1(l)*cosph2(k-l) + csl=cosph1(l)*sinph2(k-l) + cosph1ph2(l,k)=ccl-ssl + cosph1ph2(k,l)=ccl+ssl + sinph1ph2(l,k)=scl+csl + sinph1ph2(k,l)=scl-csl + enddo + enddo + if (lprn) then + write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,& + " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1 + write (iout,*) "coskt and sinkt",nntheterm_nucl + do k=1,nntheterm_nucl + write (iout,*) k,coskt(k),sinkt(k) + enddo + endif + do k=1,ntheterm_nucl + ethetai=ethetai+aathet_nucl(k,ityp1,ityp2,ityp3)*sinkt(k) + dethetai=dethetai+0.5d0*k*aathet_nucl(k,ityp1,ityp2,ityp3)& + *coskt(k) + if (lprn)& + write (iout,*) "k",k," aathet",aathet_nucl(k,ityp1,ityp2,ityp3),& + " ethetai",ethetai + enddo + if (lprn) then + write (iout,*) "cosph and sinph" + do k=1,nsingle_nucl + write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k) + enddo + write (iout,*) "cosph1ph2 and sinph2ph2" + do k=2,ndouble_nucl + do l=1,k-1 + write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),& + sinph1ph2(l,k),sinph1ph2(k,l) + enddo + enddo + write(iout,*) "ethetai",ethetai + endif + do m=1,ntheterm2_nucl + do k=1,nsingle_nucl + aux=bbthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)& + +ccthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k)& + +ddthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)& + +eethet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k) + ethetai=ethetai+sinkt(m)*aux + dethetai=dethetai+0.5d0*m*aux*coskt(m) + dephii=dephii+k*sinkt(m)*(& + ccthet_nucl(k,m,ityp1,ityp2,ityp3)*cosph1(k)-& + bbthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph1(k)) + dephii1=dephii1+k*sinkt(m)*(& + eethet_nucl(k,m,ityp1,ityp2,ityp3)*cosph2(k)-& + ddthet_nucl(k,m,ityp1,ityp2,ityp3)*sinph2(k)) + if (lprn) & + write (iout,*) "m",m," k",k," bbthet",& + bbthet_nucl(k,m,ityp1,ityp2,ityp3)," ccthet",& + ccthet_nucl(k,m,ityp1,ityp2,ityp3)," ddthet",& + ddthet_nucl(k,m,ityp1,ityp2,ityp3)," eethet",& + eethet_nucl(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai + enddo + enddo + if (lprn) & + write(iout,*) "ethetai",ethetai + do m=1,ntheterm3_nucl + do k=2,ndouble_nucl + do l=1,k-1 + aux=ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+& + ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+& + ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+& + ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l) + ethetai=ethetai+sinkt(m)*aux + dethetai=dethetai+0.5d0*m*coskt(m)*aux + dephii=dephii+l*sinkt(m)*(& + -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-& + ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+& + ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+& + ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + dephii1=dephii1+(k-l)*sinkt(m)*( & + -ffthet_nucl(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+& + ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+& + ggthet_nucl(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-& + ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)) + if (lprn) then + write (iout,*) "m",m," k",k," l",l," ffthet", & + ffthet_nucl(l,k,m,ityp1,ityp2,ityp3), & + ffthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ggthet",& + ggthet_nucl(l,k,m,ityp1,ityp2,ityp3),& + ggthet_nucl(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai + write (iout,*) cosph1ph2(l,k)*sinkt(m), & + cosph1ph2(k,l)*sinkt(m),& + sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m) + endif + enddo + enddo + enddo +10 continue + if (lprn1) write (iout,'(i2,3f8.1,9h ethetai ,f10.5)') & + i,theta(i)*rad2deg,phii*rad2deg, & + phii1*rad2deg,ethetai + etheta_nucl=etheta_nucl+ethetai +! print *,i,"partial sum",etheta_nucl + if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang_nucl*dephii + if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang_nucl*dephii1 + gloc(nphi+i-2,icg)=wang_nucl*dethetai + enddo + return + end subroutine ebend_nucl +!---------------------------------------------------- + subroutine etor_nucl(etors_nucl) +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.VAR' +! include 'COMMON.GEO' +! include 'COMMON.LOCAL' +! include 'COMMON.TORSION' +! include 'COMMON.INTERACT' +! include 'COMMON.DERIV' +! include 'COMMON.CHAIN' +! include 'COMMON.NAMES' +! include 'COMMON.IOUNITS' +! include 'COMMON.FFIELD' +! include 'COMMON.TORCNSTR' +! include 'COMMON.CONTROL' + real(kind=8) :: etors_nucl,edihcnstr + logical :: lprn +!el local variables + integer :: i,j,iblock,itori,itori1 + real(kind=8) :: phii,gloci,v1ij,v2ij,cosphi,sinphi,& + vl1ij,vl2ij,vl3ij,pom1,difi,etors_ii,pom +! Set lprn=.true. for debugging + lprn=.false. +! lprn=.true. + etors_nucl=0.0D0 +! print *,"iphi_nucl_start/end", iphi_nucl_start,iphi_nucl_end + do i=iphi_nucl_start,iphi_nucl_end + if (itype(i-2,2).eq.ntyp1_molec(2) .or. itype(i-1,2).eq.ntyp1_molec(2) & + .or. itype(i-3,2).eq.ntyp1_molec(2) & + .or. itype(i,2).eq.ntyp1_molec(2)) cycle + etors_ii=0.0D0 + itori=itortyp_nucl(itype(i-2,2)) + itori1=itortyp_nucl(itype(i-1,2)) + phii=phi(i) +! print *,i,itori,itori1 + gloci=0.0D0 +!C Regular cosine and sine terms + do j=1,nterm_nucl(itori,itori1) + v1ij=v1_nucl(j,itori,itori1) + v2ij=v2_nucl(j,itori,itori1) + cosphi=dcos(j*phii) + sinphi=dsin(j*phii) + etors_nucl=etors_nucl+v1ij*cosphi+v2ij*sinphi + if (energy_dec) etors_ii=etors_ii+& + v1ij*cosphi+v2ij*sinphi + gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi) + enddo +!C Lorentz terms +!C v1 +!C E = SUM ----------------------------------- - v1 +!C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1 +!C + cosphi=dcos(0.5d0*phii) + sinphi=dsin(0.5d0*phii) + do j=1,nlor_nucl(itori,itori1) + vl1ij=vlor1_nucl(j,itori,itori1) + vl2ij=vlor2_nucl(j,itori,itori1) + vl3ij=vlor3_nucl(j,itori,itori1) + pom=vl2ij*cosphi+vl3ij*sinphi + pom1=1.0d0/(pom*pom+1.0d0) + etors_nucl=etors_nucl+vl1ij*pom1 + if (energy_dec) etors_ii=etors_ii+ & + vl1ij*pom1 + pom=-pom*pom1*pom1 + gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom + enddo +!C Subtract the constant term + etors_nucl=etors_nucl-v0_nucl(itori,itori1) + if (energy_dec) write (iout,'(a6,i5,0pf7.3)') & + 'etor',i,etors_ii-v0_nucl(itori,itori1) + if (lprn) & + write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)') & + restyp(itype(i-2,2),2),i-2,restyp(itype(i-1,2),2),i-1,itori,itori1, & + (v1_nucl(j,itori,itori1),j=1,6),(v2_nucl(j,itori,itori1),j=1,6) + gloc(i-3,icg)=gloc(i-3,icg)+wtor_nucl*gloci +!c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg) + enddo + return + end subroutine etor_nucl +!------------------------------------------------------------ + subroutine epp_nucl_sub(evdw1,ees) +!C +!C This subroutine calculates the average interaction energy and its gradient +!C in the virtual-bond vectors between non-adjacent peptide groups, based on +!C the potential described in Liwo et al., Protein Sci., 1993, 2, 1715. +!C The potential depends both on the distance of peptide-group centers and on +!C the orientation of the CA-CA virtual bonds. +!C + integer :: i,j,k,iteli,itelj,num_conti,isubchap,ind + real(kind=8) :: dxi,dyi,dzi,dxj,dyj,dzj,aaa,bbb + real(kind=8) :: xj,yj,zj,rij,rrmij,sss,r3ij,r6ij,evdw1,& + dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi,& + dx_normj,dy_normj,dz_normj,rmij,ev1,ev2,evdwij,facvdw + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,sss_grad,fac,evdw1ij + integer xshift,yshift,zshift + real(kind=8),dimension(3):: ggg,gggp,gggm,erij + real(kind=8) :: ees,eesij +!c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions + real(kind=8) scal_el /0.5d0/ + t_eelecij=0.0d0 + ees=0.0D0 + evdw1=0.0D0 + ind=0 +!c +!c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3 +!c +! print *,"iatel_s_nucl,iatel_e_nucl",iatel_s_nucl,iatel_e_nucl + do i=iatel_s_nucl,iatel_e_nucl + if (itype(i,2).eq.ntyp1_molec(2) .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle + dxi=dc(1,i) + dyi=dc(2,i) + dzi=dc(3,i) + dx_normi=dc_norm(1,i) + dy_normi=dc_norm(2,i) + dz_normi=dc_norm(3,i) + xmedi=c(1,i)+0.5d0*dxi + ymedi=c(2,i)+0.5d0*dyi + zmedi=c(3,i)+0.5d0*dzi + xmedi=dmod(xmedi,boxxsize) + if (xmedi.lt.0) xmedi=xmedi+boxxsize + ymedi=dmod(ymedi,boxysize) + if (ymedi.lt.0) ymedi=ymedi+boxysize + zmedi=dmod(zmedi,boxzsize) + if (zmedi.lt.0) zmedi=zmedi+boxzsize + + do j=ielstart_nucl(i),ielend_nucl(i) + if (itype(j,2).eq.ntyp1_molec(2) .or. itype(j+1,2).eq.ntyp1_molec(2)) cycle + ind=ind+1 + dxj=dc(1,j) + dyj=dc(2,j) + dzj=dc(3,j) +! xj=c(1,j)+0.5D0*dxj-xmedi +! yj=c(2,j)+0.5D0*dyj-ymedi +! zj=c(3,j)+0.5D0*dzj-zmedi + xj=c(1,j)+0.5D0*dxj + yj=c(2,j)+0.5D0*dyj + zj=c(3,j)+0.5D0*dzj + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + isubchap=0 + dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + isubchap=1 + endif + enddo + enddo + enddo + if (isubchap.eq.1) then +!C print *,i,j + xj=xj_temp-xmedi + yj=yj_temp-ymedi + zj=zj_temp-zmedi + else + xj=xj_safe-xmedi + yj=yj_safe-ymedi + zj=zj_safe-zmedi + endif + + rij=xj*xj+yj*yj+zj*zj +!c write (2,*)"ij",i,j," r0pp",r0pp," rij",rij," epspp",epspp + fac=(r0pp**2/rij)**3 + ev1=epspp*fac*fac + ev2=epspp*fac + evdw1ij=ev1-2*ev2 + fac=(-ev1-evdw1ij)/rij +! write (2,*)"fac",fac," ev1",ev1," ev2",ev2," evdw1ij",evdw1ij + if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"evdw1ij",evdw1ij + evdw1=evdw1+evdw1ij +!C +!C Calculate contributions to the Cartesian gradient. +!C + ggg(1)=fac*xj + ggg(2)=fac*yj + ggg(3)=fac*zj + do k=1,3 + gvdwpp_nucl(k,i)=gvdwpp_nucl(k,i)-ggg(k) + gvdwpp_nucl(k,j)=gvdwpp_nucl(k,j)+ggg(k) + enddo +!c phoshate-phosphate electrostatic interactions + rij=dsqrt(rij) + fac=1.0d0/rij + eesij=dexp(-BEES*rij)*fac +! write (2,*)"fac",fac," eesijpp",eesij + if (energy_dec) write(iout,'(2i5,a9,f10.4)') i,j,"eesijpp",eesij + ees=ees+eesij +!c fac=-eesij*fac + fac=-(fac+BEES)*eesij*fac + ggg(1)=fac*xj + ggg(2)=fac*yj + ggg(3)=fac*zj +!c write(2,*) "ggg",i,j,ggg(1),ggg(2),ggg(3) +!c write(2,*) "gelpp",i,(gelpp(k,i),k=1,3) +!c write(2,*) "gelpp",j,(gelpp(k,j),k=1,3) + do k=1,3 + gelpp(k,i)=gelpp(k,i)-ggg(k) + gelpp(k,j)=gelpp(k,j)+ggg(k) + enddo + enddo ! j + enddo ! i +!c ees=332.0d0*ees + ees=AEES*ees + do i=nnt,nct +!c write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3) + do k=1,3 + gvdwpp_nucl(k,i)=6*gvdwpp_nucl(k,i) +!c gelpp(k,i)=332.0d0*gelpp(k,i) + gelpp(k,i)=AEES*gelpp(k,i) + enddo +!c write (2,*) "i",i," gelpp",(gelpp(k,i),k=1,3) + enddo +!c write (2,*) "total EES",ees + return + end subroutine epp_nucl_sub +!--------------------------------------------------------------------- + subroutine epsb(evdwpsb,eelpsb) +! use comm_locel +!C +!C This subroutine calculates the excluded-volume interaction energy between +!C peptide-group centers and side chains and its gradient in virtual-bond and +!C side-chain vectors. +!C + real(kind=8),dimension(3):: ggg + integer :: i,iint,j,k,iteli,itypj,subchap + real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,& + e1,e2,evdwij,rij,evdwpsb,eelpsb + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init + integer xshift,yshift,zshift + +!cd print '(a)','Enter ESCP' +!cd write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e + eelpsb=0.0d0 + evdwpsb=0.0d0 +! print *,"iatscp_s_nucl,iatscp_e_nucl",iatscp_s_nucl,iatscp_e_nucl + do i=iatscp_s_nucl,iatscp_e_nucl + if (itype(i,2).eq.ntyp1_molec(2) & + .or. itype(i+1,2).eq.ntyp1_molec(2)) cycle + xi=0.5D0*(c(1,i)+c(1,i+1)) + yi=0.5D0*(c(2,i)+c(2,i+1)) + zi=0.5D0*(c(3,i)+c(3,i+1)) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + + do iint=1,nscp_gr_nucl(i) + + do j=iscpstart_nucl(i,iint),iscpend_nucl(i,iint) + itypj=itype(j,2) + if (itypj.eq.ntyp1_molec(2)) cycle +!C Uncomment following three lines for SC-p interactions +!c xj=c(1,nres+j)-xi +!c yj=c(2,nres+j)-yi +!c zj=c(3,nres+j)-zi +!C Uncomment following three lines for Ca-p interactions +! xj=c(1,j)-xi +! yj=c(2,j)-yi +! zj=c(3,j)-zi + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + xj=mod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=mod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + + rrij=1.0D0/(xj*xj+yj*yj+zj*zj) + fac=rrij**expon2 + e1=fac*fac*aad_nucl(itypj) + e2=fac*bad_nucl(itypj) + if (iabs(j-i) .le. 2) then + e1=scal14*e1 + e2=scal14*e2 + endif + evdwij=e1+e2 + evdwpsb=evdwpsb+evdwij + if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a4)') & + 'evdw2',i,j,evdwij,"tu4" +!C +!C Calculate contributions to the gradient in the virtual-bond and SC vectors. +!C + fac=-(evdwij+e1)*rrij + ggg(1)=xj*fac + ggg(2)=yj*fac + ggg(3)=zj*fac + do k=1,3 + gvdwpsb1(k,i)=gvdwpsb1(k,i)-ggg(k) + gvdwpsb(k,j)=gvdwpsb(k,j)+ggg(k) + enddo + enddo + + enddo ! iint + enddo ! i + do i=1,nct + do j=1,3 + gvdwpsb(j,i)=expon*gvdwpsb(j,i) + gvdwpsb1(j,i)=expon*gvdwpsb1(j,i) + enddo + enddo + return + end subroutine epsb + +!------------------------------------------------------ + subroutine esb_gb(evdwsb,eelsb) + use comm_locel + use calc_data_nucl + integer :: iint,itypi,itypi1,itypj,subchap,num_conti2 + real(kind=8) :: xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi + real(kind=8) :: evdw,sig0iji,evdwsb,eelsb,ecorr,eelij + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,aa,bb,faclip,sig0ij + integer :: ii + logical lprn + evdw=0.0D0 + eelsb=0.0d0 + ecorr=0.0d0 + evdwsb=0.0D0 + lprn=.false. + ind=0 +! print *,"iastsc_nucl",iatsc_s_nucl,iatsc_e_nucl + do i=iatsc_s_nucl,iatsc_e_nucl + num_conti=0 + num_conti2=0 + itypi=itype(i,2) +! PRINT *,"I=",i,itypi + if (itypi.eq.ntyp1_molec(2)) cycle + itypi1=itype(i+1,2) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + xi=dmod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=dmod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=dmod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + + dxi=dc_norm(1,nres+i) + dyi=dc_norm(2,nres+i) + dzi=dc_norm(3,nres+i) + dsci_inv=vbld_inv(i+nres) +!C +!C Calculate SC interaction energy. +!C + do iint=1,nint_gr_nucl(i) +! print *,"tu?",i,istart_nucl(i,iint),iend_nucl(i,iint) + do j=istart_nucl(i,iint),iend_nucl(i,iint) + ind=ind+1 +! print *,"JESTEM" + itypj=itype(j,2) + if (itypj.eq.ntyp1_molec(2)) cycle + dscj_inv=vbld_inv(j+nres) + sig0ij=sigma_nucl(itypi,itypj) + chi1=chi_nucl(itypi,itypj) + chi2=chi_nucl(itypj,itypi) + chi12=chi1*chi2 + chip1=chip_nucl(itypi,itypj) + chip2=chip_nucl(itypj,itypi) + chip12=chip1*chip2 +! xj=c(1,nres+j)-xi +! yj=c(2,nres+j)-yi +! zj=c(3,nres+j)-zi + xj=c(1,nres+j) + yj=c(2,nres+j) + zj=c(3,nres+j) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + + dxj=dc_norm(1,nres+j) + dyj=dc_norm(2,nres+j) + dzj=dc_norm(3,nres+j) + rrij=1.0D0/(xj*xj+yj*yj+zj*zj) + rij=dsqrt(rrij) +!C Calculate angle-dependent terms of energy and contributions to their +!C derivatives. + erij(1)=xj*rij + erij(2)=yj*rij + erij(3)=zj*rij + om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3) + om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3) + om12=dxi*dxj+dyi*dyj+dzi*dzj + call sc_angular_nucl + sigsq=1.0D0/sigsq + sig=sig0ij*dsqrt(sigsq) + rij_shift=1.0D0/rij-sig+sig0ij +! print *,rij_shift,"rij_shift" +!c write (2,*) " rij",1.0D0/rij," sig",sig," sig0ij",sig0ij, +!c & " rij_shift",rij_shift + if (rij_shift.le.0.0D0) then + evdw=1.0D20 + return + endif + sigder=-sig*sigsq +!c--------------------------------------------------------------- + rij_shift=1.0D0/rij_shift + fac=rij_shift**expon + e1=fac*fac*aa_nucl(itypi,itypj) + e2=fac*bb_nucl(itypi,itypj) + evdwij=eps1*eps2rt*(e1+e2) +!c write (2,*) "eps1",eps1," eps2rt",eps2rt, +!c & " e1",e1," e2",e2," evdwij",evdwij + eps2der=evdwij + evdwij=evdwij*eps2rt + evdwsb=evdwsb+evdwij + if (lprn) then + sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0) + epsi=bb(itypi,itypj)**2/aa(itypi,itypj) + write (iout,'(2(a3,i3,2x),17(0pf7.3))') & + restyp(itypi,2),i,restyp(itypj,2),j, & + epsi,sigm,chi1,chi2,chip1,chip2, & + eps1,eps2rt**2,sig,sig0ij, & + om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,& + evdwij + write (iout,*) "aa",aa_nucl(itypi,itypj)," bb",bb_nucl(itypi,itypj) + endif + + if (energy_dec) write (iout,'(a6,2i5,e15.3,a4)') & + 'evdw',i,j,evdwij,"tu3" + + +!C Calculate gradient components. + e1=e1*eps1*eps2rt**2 + fac=-expon*(e1+evdwij)*rij_shift + sigder=fac*sigder + fac=rij*fac +!c fac=0.0d0 +!C Calculate the radial part of the gradient + gg(1)=xj*fac + gg(2)=yj*fac + gg(3)=zj*fac +!C Calculate angular part of the gradient. + call sc_grad_nucl + call eelsbij(eelij,num_conti2) + if (energy_dec .and. & + (j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2)) & + write (istat,'(e14.5)') evdwij + eelsb=eelsb+eelij + enddo ! j + enddo ! iint + num_cont_hb(i)=num_conti2 + enddo ! i +!c write (iout,*) "Number of loop steps in EGB:",ind +!cccc energy_dec=.false. + return + end subroutine esb_gb +!------------------------------------------------------------------------------- + subroutine eelsbij(eesij,num_conti2) + use comm_locel + use calc_data_nucl + real(kind=8),dimension(3) :: ggg,gggp,gggm,dcosb,dcosg + real(kind=8),dimension(3,3) :: erder,uryg,urzg,vryg,vrzg + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,rlocshield,fracinbuf + integer xshift,yshift,zshift,ilist,iresshield,num_conti2 + +!c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions + real(kind=8) scal_el /0.5d0/ + integer :: iteli,itelj,kkk,kkll,m,isubchap + real(kind=8) :: ael6i,rrmij,rmij,r0ij,fcont,fprimcont,ees0tmp,facfac + real(kind=8) :: ees,evdw1,eel_loc,aaa,bbb,ael3i,ael63i,ael32i + real(kind=8) :: dx_normj,dy_normj,dz_normj,& + r3ij,r6ij,cosa,cosb,cosg,fac,ev1,ev2,fac3,fac4,fac5,fac6,& + el1,el2,el3,el4,eesij,ees0ij,facvdw,facel,fac1,ecosa,& + ecosb,ecosg,ury,urz,vry,vrz,facr,a22der,a23der,a32der,& + a33der,eel_loc_ij,cosa4,wij,cosbg1,cosbg2,ees0pij,& + ees0pij1,ees0mij,ees0mij1,fac3p,ees0mijp,ees0pijp,& + ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,& + ecosgp,ecosam,ecosbm,ecosgm,ghalf,itypi,itypj + ind=ind+1 + itypi=itype(i,2) + itypj=itype(j,2) +! print *,i,j,itypi,itypj,istype(i),istype(j),"????" + ael6i=ael6_nucl(itypi,itypj) + ael3i=ael3_nucl(itypi,itypj) + ael63i=ael63_nucl(itypi,itypj) + ael32i=ael32_nucl(itypi,itypj) +!c write (iout,*) "eelecij",i,j,itype(i),itype(j), +!c & ael6i,ael3i,ael63i,al32i,rij,rrij + dxj=dc(1,j+nres) + dyj=dc(2,j+nres) + dzj=dc(3,j+nres) + dx_normi=dc_norm(1,i+nres) + dy_normi=dc_norm(2,i+nres) + dz_normi=dc_norm(3,i+nres) + dx_normj=dc_norm(1,j+nres) + dy_normj=dc_norm(2,j+nres) + dz_normj=dc_norm(3,j+nres) +!c xj=c(1,j)+0.5D0*dxj-xmedi +!c yj=c(2,j)+0.5D0*dyj-ymedi +!c zj=c(3,j)+0.5D0*dzj-zmedi + if (ipot_nucl.ne.2) then + cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj + cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij + cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij + else + cosa=om12 + cosb=om1 + cosg=om2 + endif + r3ij=rij*rrij + r6ij=r3ij*r3ij + fac=cosa-3.0D0*cosb*cosg + facfac=fac*fac + fac1=3.0d0*(cosb*cosb+cosg*cosg) + fac3=ael6i*r6ij + fac4=ael3i*r3ij + fac5=ael63i*r6ij + fac6=ael32i*r6ij +!c write (iout,*) "r3ij",r3ij," r6ij",r6ij," fac",fac," fac1",fac1, +!c & " fac2",fac2," fac3",fac3," fac4",fac4," fac5",fac5," fac6",fac6 + el1=fac3*(4.0D0+facfac-fac1) + el2=fac4*fac + el3=fac5*(2.0d0-2.0d0*facfac+fac1) + el4=fac6*facfac + eesij=el1+el2+el3+el4 +!C 12/26/95 - for the evaluation of multi-body H-bonding interactions + ees0ij=4.0D0+facfac-fac1 + + if (energy_dec) then + if(j.eq.i+1.or.j.eq.nres-i+1.or.j.eq.nres-i.or.j.eq.nres-i+2) & + write (istat,'(2a1,i4,1x,2a1,i4,4f10.5,3e12.5,$)') & + sugartyp(istype(i)),restyp(itypi,2),i,sugartyp(istype(j)),& + restyp(itypj,2),j,1.0d0/rij,cosa,cosb,cosg,fac*r3ij, & + (4.0D0+facfac-fac1)*r6ij,(2.0d0-2.0d0*facfac+fac1)*r6ij + write (iout,'(a6,2i5,e15.3)') 'ees',i,j,eesij + endif + +!C +!C Calculate contributions to the Cartesian gradient. +!C + facel=-3.0d0*rrij*(eesij+el1+el3+el4) + fac1=fac +!c erij(1)=xj*rmij +!c erij(2)=yj*rmij +!c erij(3)=zj*rmij +!* +!* Radial derivatives. First process both termini of the fragment (i,j) +!* + ggg(1)=facel*xj + ggg(2)=facel*yj + ggg(3)=facel*zj + do k=1,3 + gelsbc(k,j)=gelsbc(k,j)+ggg(k) + gelsbc(k,i)=gelsbc(k,i)-ggg(k) + gelsbx(k,j)=gelsbx(k,j)+ggg(k) + gelsbx(k,i)=gelsbx(k,i)-ggg(k) + enddo +!* +!* Angular part +!* + ecosa=2.0D0*fac3*fac1+fac4+(-4.0d0*fac5+2.0d0*fac6)*fac1 + fac4=-3.0D0*fac4 + fac3=-6.0D0*fac3 + fac5= 6.0d0*fac5 + fac6=-6.0d0*fac6 + ecosb=fac3*(fac1*cosg+cosb)+cosg*fac4+(cosb+2*fac1*cosg)*fac5+& + fac6*fac1*cosg + ecosg=fac3*(fac1*cosb+cosg)+cosb*fac4+(cosg+2*fac1*cosb)*fac5+& + fac6*fac1*cosb + do k=1,3 + dcosb(k)=rij*(dc_norm(k,i+nres)-erij(k)*cosb) + dcosg(k)=rij*(dc_norm(k,j+nres)-erij(k)*cosg) + enddo + do k=1,3 + ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k) + enddo + do k=1,3 + gelsbx(k,i)=gelsbx(k,i)-ggg(k) & + +(ecosa*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres))& + + ecosb*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres) + gelsbx(k,j)=gelsbx(k,j)+ggg(k) & + +(ecosa*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))& + + ecosg*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres) + gelsbc(k,j)=gelsbc(k,j)+ggg(k) + gelsbc(k,i)=gelsbc(k,i)-ggg(k) + enddo +! IF ( (wcorr_nucl.gt.0.0d0.or.wcorr3_nucl.gt.0.0d0) .and. + IF ( j.gt.i+1 .and.& + num_conti.le.maxconts) THEN +!C +!C Calculate the contact function. The ith column of the array JCONT will +!C contain the numbers of atoms that make contacts with the atom I (of numbers +!C greater than I). The arrays FACONT and GACONT will contain the values of +!C the contact function and its derivative. + r0ij=2.20D0*sigma(itypi,itypj) +!c write (2,*) "ij",i,j," rij",1.0d0/rij," r0ij",r0ij + call gcont(rij,r0ij,1.0D0,0.2d0/r0ij,fcont,fprimcont) +!c write (2,*) "fcont",fcont + if (fcont.gt.0.0D0) then + num_conti=num_conti+1 + num_conti2=num_conti2+1 + + if (num_conti.gt.maxconts) then + write (iout,*) 'WARNING - max. # of contacts exceeded;',& + ' will skip next contacts for this conf.' + else + jcont_hb(num_conti,i)=j +!c write (iout,*) "num_conti",num_conti, +!c & " jcont_hb",jcont_hb(num_conti,i) +!C Calculate contact energies + cosa4=4.0D0*cosa + wij=cosa-3.0D0*cosb*cosg + cosbg1=cosb+cosg + cosbg2=cosb-cosg + fac3=dsqrt(-ael6i)*r3ij +!c write (2,*) "ael6i",ael6i," r3ij",r3ij," fac3",fac3 + ees0tmp=4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1 + if (ees0tmp.gt.0) then + ees0pij=dsqrt(ees0tmp) + else + ees0pij=0 + endif + ees0tmp=4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2 + if (ees0tmp.gt.0) then + ees0mij=dsqrt(ees0tmp) + else + ees0mij=0 + endif + ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij) + ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij) +!c write (iout,*) "i",i," j",j, +!c & " ees0m",ees0m(num_conti,i)," ees0p",ees0p(num_conti,i) + ees0pij1=fac3/ees0pij + ees0mij1=fac3/ees0mij + fac3p=-3.0D0*fac3*rrij + ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij) + ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij) + ecosa1= ees0pij1*( 1.0D0+0.5D0*wij) + ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1) + ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1) + ecosa2= ees0mij1*(-1.0D0+0.5D0*wij) + ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2) + ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2) + ecosap=ecosa1+ecosa2 + ecosbp=ecosb1+ecosb2 + ecosgp=ecosg1+ecosg2 + ecosam=ecosa1-ecosa2 + ecosbm=ecosb1-ecosb2 + ecosgm=ecosg1-ecosg2 +!C End diagnostics + facont_hb(num_conti,i)=fcont + fprimcont=fprimcont/rij + do k=1,3 + gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k) + gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k) + enddo + gggp(1)=gggp(1)+ees0pijp*xj + gggp(2)=gggp(2)+ees0pijp*yj + gggp(3)=gggp(3)+ees0pijp*zj + gggm(1)=gggm(1)+ees0mijp*xj + gggm(2)=gggm(2)+ees0mijp*yj + gggm(3)=gggm(3)+ees0mijp*zj +!C Derivatives due to the contact function + gacont_hbr(1,num_conti,i)=fprimcont*xj + gacont_hbr(2,num_conti,i)=fprimcont*yj + gacont_hbr(3,num_conti,i)=fprimcont*zj + do k=1,3 +!c +!c Gradient of the correlation terms +!c + gacontp_hb1(k,num_conti,i)= & + (ecosap*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) & + + ecosbp*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres) + gacontp_hb2(k,num_conti,i)= & + (ecosap*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres)) & + + ecosgp*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres) + gacontp_hb3(k,num_conti,i)=gggp(k) + gacontm_hb1(k,num_conti,i)= & + (ecosam*(dc_norm(k,j+nres)-cosa*dc_norm(k,i+nres)) & + + ecosbm*(erij(k)-cosb*dc_norm(k,i+nres)))*vbld_inv(i+nres) + gacontm_hb2(k,num_conti,i)= & + (ecosam*(dc_norm(k,i+nres)-cosa*dc_norm(k,j+nres))& + + ecosgm*(erij(k)-cosg*dc_norm(k,j+nres)))*vbld_inv(j+nres) + gacontm_hb3(k,num_conti,i)=gggm(k) + enddo + endif + endif + ENDIF + return + end subroutine eelsbij +!------------------------------------------------------------------ + subroutine sc_grad_nucl + use comm_locel + use calc_data_nucl + real(kind=8),dimension(3) :: dcosom1,dcosom2 + eom1=eps2der*eps2rt_om1+sigder*sigsq_om1 + eom2=eps2der*eps2rt_om2+sigder*sigsq_om2 + eom12=evdwij*eps1_om12+eps2der*eps2rt_om12+sigder*sigsq_om12 + do k=1,3 + dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k)) + dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k)) + enddo + do k=1,3 + gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k) + enddo + do k=1,3 + gvdwsbx(k,i)=gvdwsbx(k,i)-gg(k) & + +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))& + +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv + gvdwsbx(k,j)=gvdwsbx(k,j)+gg(k) & + +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & + +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + enddo +!C +!C Calculate the components of the gradient in DC and X +!C + do l=1,3 + gvdwsbc(l,i)=gvdwsbc(l,i)-gg(l) + gvdwsbc(l,j)=gvdwsbc(l,j)+gg(l) + enddo + return + end subroutine sc_grad_nucl +!----------------------------------------------------------------------- + subroutine esb(esbloc) +!C Calculate the local energy of a side chain and its derivatives in the +!C corresponding virtual-bond valence angles THETA and the spherical angles +!C ALPHA and OMEGA derived from AM1 all-atom calculations. +!C added by Urszula Kozlowska. 07/11/2007 +!C + real(kind=8),dimension(3):: x_prime,y_prime,z_prime + real(kind=8),dimension(9):: x + real(kind=8) :: sumene,dsc_i,dp2_i,xx,yy,zz,sumene1, & + sumene2,sumene3,sumene4,s1,s1_6,s2,s2_6,& + de_dxx,de_dyy,de_dzz,de_dt,s1_t,s1_6_t,s2_t,s2_6_t + real(kind=8),dimension(3):: dXX_Ci1,dYY_Ci1,dZZ_Ci1,dXX_Ci,& + dYY_Ci,dZZ_Ci,dXX_XYZ,dYY_XYZ,dZZ_XYZ,dt_dCi,dt_dCi1 + real(kind=8) :: esbloc,delta,cosfac2,cosfac,sinfac2,sinfac,de_dtt,& + cossc,cossc1,cosfac2xx,sinfac2yy,pom1,pom + integer::it,nlobit,i,j,k +! common /sccalc/ time11,time12,time112,theti,it,nlobit + delta=0.02d0*pi + esbloc=0.0D0 + do i=loc_start_nucl,loc_end_nucl + if (itype(i,2).eq.ntyp1_molec(2)) cycle + costtab(i+1) =dcos(theta(i+1)) + sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1)) + cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1))) + sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1))) + cosfac2=0.5d0/(1.0d0+costtab(i+1)) + cosfac=dsqrt(cosfac2) + sinfac2=0.5d0/(1.0d0-costtab(i+1)) + sinfac=dsqrt(sinfac2) + it=itype(i,2) + if (it.eq.10) goto 1 + +!c +!C Compute the axes of tghe local cartesian coordinates system; store in +!c x_prime, y_prime and z_prime +!c + do j=1,3 + x_prime(j) = 0.00 + y_prime(j) = 0.00 + z_prime(j) = 0.00 + enddo +!C write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres), +!C & dc_norm(3,i+nres) + do j = 1,3 + x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac + y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac + enddo + do j = 1,3 + z_prime(j) = -uz(j,i-1) +! z_prime(j)=0.0 + enddo + + xx=0.0d0 + yy=0.0d0 + zz=0.0d0 + do j = 1,3 + xx = xx + x_prime(j)*dc_norm(j,i+nres) + yy = yy + y_prime(j)*dc_norm(j,i+nres) + zz = zz + z_prime(j)*dc_norm(j,i+nres) + enddo + + xxtab(i)=xx + yytab(i)=yy + zztab(i)=zz + it=itype(i,2) + do j = 1,9 + x(j) = sc_parmin_nucl(j,it) + enddo +#ifdef CHECK_COORD +!Cc diagnostics - remove later + xx1 = dcos(alph(2)) + yy1 = dsin(alph(2))*dcos(omeg(2)) + zz1 = -dsin(alph(2))*dsin(omeg(2)) + write(2,'(3f8.1,3f9.3,1x,3f9.3)') & + alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,& + xx1,yy1,zz1 +!C," --- ", xx_w,yy_w,zz_w +!c end diagnostics +#endif + sumene = enesc_nucl(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) + esbloc = esbloc + sumene + sumene2= enesc_nucl(x,xx,yy,0.0d0,cost2tab(i+1),sint2tab(i+1)) +! print *,"enecomp",sumene,sumene2 +! if (energy_dec) write(iout,*) "i",i," esbloc",sumene,esbloc,xx,yy,zz +! if (energy_dec) write(iout,*) "x",(x(k),k=1,9) +#ifdef DEBUG + write (2,*) "x",(x(k),k=1,9) +!C +!C This section to check the numerical derivatives of the energy of ith side +!C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert +!C #define DEBUG in the code to turn it on. +!C + write (2,*) "sumene =",sumene + aincr=1.0d-7 + xxsave=xx + xx=xx+aincr + write (2,*) xx,yy,zz + sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) + de_dxx_num=(sumenep-sumene)/aincr + xx=xxsave + write (2,*) "xx+ sumene from enesc=",sumenep,sumene + yysave=yy + yy=yy+aincr + write (2,*) xx,yy,zz + sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) + de_dyy_num=(sumenep-sumene)/aincr + yy=yysave + write (2,*) "yy+ sumene from enesc=",sumenep,sumene + zzsave=zz + zz=zz+aincr + write (2,*) xx,yy,zz + sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) + de_dzz_num=(sumenep-sumene)/aincr + zz=zzsave + write (2,*) "zz+ sumene from enesc=",sumenep,sumene + costsave=cost2tab(i+1) + sintsave=sint2tab(i+1) + cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr)) + sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr)) + sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1)) + de_dt_num=(sumenep-sumene)/aincr + write (2,*) " t+ sumene from enesc=",sumenep,sumene + cost2tab(i+1)=costsave + sint2tab(i+1)=sintsave +!C End of diagnostics section. +#endif +!C +!C Compute the gradient of esc +!C + de_dxx=x(1)+2*x(4)*xx+x(7)*zz+x(8)*yy + de_dyy=x(2)+2*x(5)*yy+x(8)*xx+x(9)*zz + de_dzz=x(3)+2*x(6)*zz+x(7)*xx+x(9)*yy + de_dtt=0.0d0 +#ifdef DEBUG + write (2,*) "x",(x(k),k=1,9) + write (2,*) "xx",xx," yy",yy," zz",zz + write (2,*) "de_xx ",de_xx," de_yy ",de_yy,& + " de_zz ",de_zz," de_tt ",de_tt + write (2,*) "de_xx_num",de_dxx_num," de_yy_num",de_dyy_num,& + " de_zz_num",de_dzz_num," de_dt_num",de_dt_num +#endif +!C + cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres)) + cossc1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres)) + cosfac2xx=cosfac2*xx + sinfac2yy=sinfac2*yy + do k = 1,3 + dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*& + vbld_inv(i+1) + dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*& + vbld_inv(i) + pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1) + pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i) +!c write (iout,*) "i",i," k",k," pom",pom," pom1",pom1, +!c & " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k) +!c write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3), +!c & (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i) + dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx + dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx + dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy + dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy + dZZ_Ci1(k)=0.0d0 + dZZ_Ci(k)=0.0d0 + do j=1,3 + dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres) + dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres) + enddo + + dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres)) + dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres)) + dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres)) +!c + dt_dCi(k) = -dt_dCi(k)/sinttab(i+1) + dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1) + enddo + + do k=1,3 + dXX_Ctab(k,i)=dXX_Ci(k) + dXX_C1tab(k,i)=dXX_Ci1(k) + dYY_Ctab(k,i)=dYY_Ci(k) + dYY_C1tab(k,i)=dYY_Ci1(k) + dZZ_Ctab(k,i)=dZZ_Ci(k) + dZZ_C1tab(k,i)=dZZ_Ci1(k) + dXX_XYZtab(k,i)=dXX_XYZ(k) + dYY_XYZtab(k,i)=dYY_XYZ(k) + dZZ_XYZtab(k,i)=dZZ_XYZ(k) + enddo + do k = 1,3 +!c write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1", +!c & dyy_ci1(k)," dzz_ci1",dzz_ci1(k) +!c write (iout,*) "k",k," dxx_ci",dxx_ci(k)," dyy_ci", +!c & dyy_ci(k)," dzz_ci",dzz_ci(k) +!c write (iout,*) "k",k," dt_dci",dt_dci(k)," dt_dci", +!c & dt_dci(k) +!c write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ", +!c & dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k) + gsbloc(k,i-1)=gsbloc(k,i-1)+(de_dxx*dxx_ci1(k) & + +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k)) + gsbloc(k,i)=gsbloc(k,i)+(de_dxx*dxx_Ci(k) & + +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k)) + gsblocx(k,i)= de_dxx*dxx_XYZ(k)& + +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k) +! print *,i,de_dxx*dxx_ci1(k)+de_dyy*dyy_ci1(k),de_dzz*dzz_ci1(k)*2 + enddo +!c write(iout,*) "ENERGY GRAD = ", (gsbloc(k,i-1),k=1,3), +!c & (gsbloc(k,i),k=1,3),(gsblocx(k,i),k=1,3) + +!C to check gradient call subroutine check_grad + + 1 continue + enddo + return + end subroutine esb +!=------------------------------------------------------- + real(kind=8) function enesc_nucl(x,xx,yy,zz,cost2,sint2) +! implicit none + real(kind=8),dimension(9):: x(9) + real(kind=8) :: xx,yy,zz,cost2,sint2,sumene1,sumene2, & + sumene3,sumene4,sumene,dsc_i,dp2_i,dscp1,dscp2,s1,s1_6,s2,s2_6 + integer i +!c write (2,*) "enesc" +!c write (2,*) "x",(x(i),i=1,9) +!c write(2,*)"xx",xx," yy",yy," zz",zz," cost2",cost2," sint2",sint2 + sumene=x(1)*xx+x(2)*yy+x(3)*zz+x(4)*xx**2 & + + x(5)*yy**2+x(6)*zz**2+x(7)*xx*zz+x(8)*xx*yy & + + x(9)*yy*zz + enesc_nucl=sumene + return + end function enesc_nucl +!----------------------------------------------------------------------------- + subroutine multibody_hb_nucl(ecorr,ecorr3,n_corr,n_corr1) +#ifdef MPI + include 'mpif.h' + integer,parameter :: max_cont=2000 + integer,parameter:: max_dim=2*(8*3+6) + integer, parameter :: msglen1=max_cont*max_dim + integer,parameter :: msglen2=2*msglen1 + integer source,CorrelType,CorrelID,Error + real(kind=8) :: buffer(max_cont,max_dim) + integer status(MPI_STATUS_SIZE) + integer :: ierror,nbytes +#endif + real(kind=8),dimension(3):: gx(3),gx1(3) + real(kind=8) :: time00 + logical lprn,ldone + integer i,j,i1,j1,jj,kk,num_conti,num_conti1,nn + real(kind=8) ecorr,ecorr3 + integer :: n_corr,n_corr1,mm,msglen +!C Set lprn=.true. for debugging + lprn=.false. + n_corr=0 + n_corr1=0 +#ifdef MPI + if(.not.allocated(zapas2)) allocate(zapas2(3,maxconts,nres,8)) + + if (nfgtasks.le.1) goto 30 + if (lprn) then + write (iout,'(a)') 'Contact function values:' + do i=nnt,nct-1 + write (iout,'(2i3,50(1x,i2,f5.2))') & + i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), & + j=1,num_cont_hb(i)) + enddo + endif +!C Caution! Following code assumes that electrostatic interactions concerning +!C a given atom are split among at most two processors! + CorrelType=477 + CorrelID=fg_rank+1 + ldone=.false. + do i=1,max_cont + do j=1,max_dim + buffer(i,j)=0.0D0 + enddo + enddo + mm=mod(fg_rank,2) +!c write (*,*) 'MyRank',MyRank,' mm',mm + if (mm) 20,20,10 + 10 continue +!c write (*,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone + if (fg_rank.gt.0) then +!C Send correlation contributions to the preceding processor + msglen=msglen1 + nn=num_cont_hb(iatel_s_nucl) + call pack_buffer(max_cont,max_dim,iatel_s,0,buffer) +!c write (*,*) 'The BUFFER array:' +!c do i=1,nn +!c write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,30) +!c enddo + if (ielstart_nucl(iatel_s_nucl).gt.iatel_s_nucl+ispp) then + msglen=msglen2 + call pack_buffer(max_cont,max_dim,iatel_s+1,30,buffer) +!C Clear the contacts of the atom passed to the neighboring processor + nn=num_cont_hb(iatel_s_nucl+1) +!c do i=1,nn +!c write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j+30),j=1,30) +!c enddo + num_cont_hb(iatel_s_nucl)=0 + endif +!cd write (iout,*) 'Processor ',fg_rank,MyRank, +!cd & ' is sending correlation contribution to processor',fg_rank-1, +!cd & ' msglen=',msglen +!c write (*,*) 'Processor ',fg_rank,MyRank, +!c & ' is sending correlation contribution to processor',fg_rank-1, +!c & ' msglen=',msglen,' CorrelType=',CorrelType + time00=MPI_Wtime() + call MPI_Send(buffer,msglen,MPI_DOUBLE_PRECISION,fg_rank-1, & + CorrelType,FG_COMM,IERROR) + time_sendrecv=time_sendrecv+MPI_Wtime()-time00 +!cd write (iout,*) 'Processor ',fg_rank, +!cd & ' has sent correlation contribution to processor',fg_rank-1, +!cd & ' msglen=',msglen,' CorrelID=',CorrelID +!c write (*,*) 'Processor ',fg_rank, +!c & ' has sent correlation contribution to processor',fg_rank-1, +!c & ' msglen=',msglen,' CorrelID=',CorrelID +!c msglen=msglen1 + endif ! (fg_rank.gt.0) + if (ldone) goto 30 + ldone=.true. + 20 continue +!c write (*,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone + if (fg_rank.lt.nfgtasks-1) then +!C Receive correlation contributions from the next processor + msglen=msglen1 + if (ielend_nucl(iatel_e_nucl).lt.nct_molec(2)-1) msglen=msglen2 +!cd write (iout,*) 'Processor',fg_rank, +!cd & ' is receiving correlation contribution from processor',fg_rank+1, +!cd & ' msglen=',msglen,' CorrelType=',CorrelType +!c write (*,*) 'Processor',fg_rank, +!c &' is receiving correlation contribution from processor',fg_rank+1, +!c & ' msglen=',msglen,' CorrelType=',CorrelType + time00=MPI_Wtime() + nbytes=-1 + do while (nbytes.le.0) + call MPI_Probe(fg_rank+1,CorrelType,FG_COMM,status,IERROR) + call MPI_Get_count(status,MPI_DOUBLE_PRECISION,nbytes,IERROR) + enddo +!c print *,'Processor',myrank,' msglen',msglen,' nbytes',nbytes + call MPI_Recv(buffer,nbytes,MPI_DOUBLE_PRECISION, & + fg_rank+1,CorrelType,FG_COMM,status,IERROR) + time_sendrecv=time_sendrecv+MPI_Wtime()-time00 +!c write (*,*) 'Processor',fg_rank, +!c &' has received correlation contribution from processor',fg_rank+1, +!c & ' msglen=',msglen,' nbytes=',nbytes +!c write (*,*) 'The received BUFFER array:' +!c do i=1,max_cont +!c write (*,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,60) +!c enddo + if (msglen.eq.msglen1) then + call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,0,buffer) + else if (msglen.eq.msglen2) then + call unpack_buffer(max_cont,max_dim,iatel_e_nucl,0,buffer) + call unpack_buffer(max_cont,max_dim,iatel_e_nucl+1,30,buffer) + else + write (iout,*) & + 'ERROR!!!! message length changed while processing correlations.' + write (*,*) & + 'ERROR!!!! message length changed while processing correlations.' + call MPI_Abort(MPI_COMM_WORLD,Error,IERROR) + endif ! msglen.eq.msglen1 + endif ! fg_rank.lt.nfgtasks-1 + if (ldone) goto 30 + ldone=.true. + goto 10 + 30 continue +#endif + if (lprn) then + write (iout,'(a)') 'Contact function values:' + do i=nnt_molec(2),nct_molec(2)-1 + write (iout,'(2i3,50(1x,i2,f5.2))') & + i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i), & + j=1,num_cont_hb(i)) + enddo + endif + ecorr=0.0D0 + ecorr3=0.0d0 +!C Remove the loop below after debugging !!! +! do i=nnt_molec(2),nct_molec(2) +! do j=1,3 +! gradcorr_nucl(j,i)=0.0D0 +! gradxorr_nucl(j,i)=0.0D0 +! gradcorr3_nucl(j,i)=0.0D0 +! gradxorr3_nucl(j,i)=0.0D0 +! enddo +! enddo +! print *,"iatsc_s_nucl,iatsc_e_nucl",iatsc_s_nucl,iatsc_e_nucl +!C Calculate the local-electrostatic correlation terms + do i=iatsc_s_nucl,iatsc_e_nucl + i1=i+1 + num_conti=num_cont_hb(i) + num_conti1=num_cont_hb(i+1) +! print *,i,num_conti,num_conti1 + do jj=1,num_conti + j=jcont_hb(jj,i) + do kk=1,num_conti1 + j1=jcont_hb(kk,i1) +!c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1, +!c & ' jj=',jj,' kk=',kk + if (j1.eq.j+1 .or. j1.eq.j-1) then +!C +!C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously. +!C The system gains extra energy. +!C Tentative expression & coefficients; assumed d(stacking)=4.5 A, +!C parallel dipoles of stacknig bases and sin(mui)sin(muj)/eps/d^3=0.7 +!C Need to implement full formulas 34 and 35 from Liwo et al., 1998. +!C + ecorr=ecorr+ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0) + if (energy_dec) write (iout,'(a6,2i5,0pf7.3)') & + 'ecorrh',i,j,ehbcorr_nucl(i,j,i+1,j1,jj,kk,0.528D0,0.132D0) + n_corr=n_corr+1 + else if (j1.eq.j) then +!C +!C Contacts I-J and I-(J+1) occur simultaneously. +!C The system loses extra energy. +!C Tentative expression & c?oefficients; assumed d(stacking)=4.5 A, +!C parallel dipoles of stacknig bases and sin(mui)sin(muj)/eps/d^3=0.7 +!C Need to implement full formulas 32 from Liwo et al., 1998. +!C +!c write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1, +!c & ' jj=',jj,' kk=',kk + ecorr3=ecorr3+ehbcorr3_nucl(i,j,i+1,j,jj,kk,0.310D0,-0.155D0) + endif + enddo ! kk + do kk=1,num_conti + j1=jcont_hb(kk,i) +!c write (iout,*) 'ecorr3: i=',i,' j=',j,' i1=',i1,' j1=',j1, +!c & ' jj=',jj,' kk=',kk + if (j1.eq.j+1) then +!C Contacts I-J and (I+1)-J occur simultaneously. +!C The system loses extra energy. + ecorr3=ecorr3+ehbcorr3_nucl(i,j,i,j+1,jj,kk,0.310D0,-0.155D0) + endif ! j1==j+1 + enddo ! kk + enddo ! jj + enddo ! i + return + end subroutine multibody_hb_nucl +!----------------------------------------------------------- + real(kind=8) function ehbcorr_nucl(i,j,k,l,jj,kk,coeffp,coeffm) +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.IOUNITS' +! include 'COMMON.DERIV' +! include 'COMMON.INTERACT' +! include 'COMMON.CONTACTS' + real(kind=8),dimension(3) :: gx,gx1 + logical :: lprn +!el local variables + integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield + real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,& + ees0mkl,ees,coeffpees0pij,coeffmees0mij,& + coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, & + rlocshield + + lprn=.false. + eij=facont_hb(jj,i) + ekl=facont_hb(kk,k) + ees0pij=ees0p(jj,i) + ees0pkl=ees0p(kk,k) + ees0mij=ees0m(jj,i) + ees0mkl=ees0m(kk,k) + ekont=eij*ekl + ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl) +! print *,"ehbcorr_nucl",ekont,ees +!cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl) +!C Following 4 lines for diagnostics. +!cd ees0pkl=0.0D0 +!cd ees0pij=1.0D0 +!cd ees0mkl=0.0D0 +!cd ees0mij=1.0D0 +!cd write (iout,*)'Contacts have occurred for nucleic bases', +!cd & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l +!cd & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees +!C Calculate the multi-body contribution to energy. +! ecorr_nucl=ecorr_nucl+ekont*ees +!C Calculate multi-body contributions to the gradient. + coeffpees0pij=coeffp*ees0pij + coeffmees0mij=coeffm*ees0mij + coeffpees0pkl=coeffp*ees0pkl + coeffmees0mkl=coeffm*ees0mkl + do ll=1,3 + gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i) & + -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+& + coeffmees0mkl*gacontm_hb1(ll,jj,i)) + gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j) & + -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+& + coeffmees0mkl*gacontm_hb2(ll,jj,i)) + gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k) & + -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+& + coeffmees0mij*gacontm_hb1(ll,kk,k)) + gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l) & + -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ & + coeffmees0mij*gacontm_hb2(ll,kk,k)) + gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- & + ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ & + coeffmees0mkl*gacontm_hb3(ll,jj,i)) + gradcorr_nucl(ll,j)=gradcorr_nucl(ll,j)+gradlongij + gradcorr_nucl(ll,i)=gradcorr_nucl(ll,i)-gradlongij + gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- & + ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ & + coeffmees0mij*gacontm_hb3(ll,kk,k)) + gradcorr_nucl(ll,l)=gradcorr_nucl(ll,l)+gradlongkl + gradcorr_nucl(ll,k)=gradcorr_nucl(ll,k)-gradlongkl + gradxorr_nucl(ll,i)=gradxorr_nucl(ll,i)-gradlongij + gradxorr_nucl(ll,j)=gradxorr_nucl(ll,j)+gradlongij + gradxorr_nucl(ll,k)=gradxorr_nucl(ll,k)-gradlongkl + gradxorr_nucl(ll,l)=gradxorr_nucl(ll,l)+gradlongkl + enddo + ehbcorr_nucl=ekont*ees + return + end function ehbcorr_nucl +!------------------------------------------------------------------------- + + real(kind=8) function ehbcorr3_nucl(i,j,k,l,jj,kk,coeffp,coeffm) +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.IOUNITS' +! include 'COMMON.DERIV' +! include 'COMMON.INTERACT' +! include 'COMMON.CONTACTS' + real(kind=8),dimension(3) :: gx,gx1 + logical :: lprn +!el local variables + integer :: i,j,k,l,jj,kk,ll,ilist,m, iresshield + real(kind=8) :: coeffp,coeffm,eij,ekl,ees0pij,ees0pkl,ees0mij,& + ees0mkl,ees,coeffpees0pij,coeffmees0mij,& + coeffpees0pkl,coeffmees0mkl,gradlongij,gradlongkl, & + rlocshield + + lprn=.false. + eij=facont_hb(jj,i) + ekl=facont_hb(kk,k) + ees0pij=ees0p(jj,i) + ees0pkl=ees0p(kk,k) + ees0mij=ees0m(jj,i) + ees0mkl=ees0m(kk,k) + ekont=eij*ekl + ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl) +!cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl) +!C Following 4 lines for diagnostics. +!cd ees0pkl=0.0D0 +!cd ees0pij=1.0D0 +!cd ees0mkl=0.0D0 +!cd ees0mij=1.0D0 +!cd write (iout,*)'Contacts have occurred for nucleic bases', +!cd & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l +!cd & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees +!C Calculate the multi-body contribution to energy. +! ecorr=ecorr+ekont*ees +!C Calculate multi-body contributions to the gradient. + coeffpees0pij=coeffp*ees0pij + coeffmees0mij=coeffm*ees0mij + coeffpees0pkl=coeffp*ees0pkl + coeffmees0mkl=coeffm*ees0mkl + do ll=1,3 + gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i) & + -ekont*(coeffpees0pkl*gacontp_hb1(ll,jj,i)+& + coeffmees0mkl*gacontm_hb1(ll,jj,i)) + gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j) & + -ekont*(coeffpees0pkl*gacontp_hb2(ll,jj,i)+ & + coeffmees0mkl*gacontm_hb2(ll,jj,i)) + gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k) & + -ekont*(coeffpees0pij*gacontp_hb1(ll,kk,k)+ & + coeffmees0mij*gacontm_hb1(ll,kk,k)) + gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l) & + -ekont*(coeffpees0pij*gacontp_hb2(ll,kk,k)+ & + coeffmees0mij*gacontm_hb2(ll,kk,k)) + gradlongij=ees*ekl*gacont_hbr(ll,jj,i)- & + ekont*(coeffpees0pkl*gacontp_hb3(ll,jj,i)+ & + coeffmees0mkl*gacontm_hb3(ll,jj,i)) + gradcorr3_nucl(ll,j)=gradcorr3_nucl(ll,j)+gradlongij + gradcorr3_nucl(ll,i)=gradcorr3_nucl(ll,i)-gradlongij + gradlongkl=ees*eij*gacont_hbr(ll,kk,k)- & + ekont*(coeffpees0pij*gacontp_hb3(ll,kk,k)+ & + coeffmees0mij*gacontm_hb3(ll,kk,k)) + gradcorr3_nucl(ll,l)=gradcorr3_nucl(ll,l)+gradlongkl + gradcorr3_nucl(ll,k)=gradcorr3_nucl(ll,k)-gradlongkl + gradxorr3_nucl(ll,i)=gradxorr3_nucl(ll,i)-gradlongij + gradxorr3_nucl(ll,j)=gradxorr3_nucl(ll,j)+gradlongij + gradxorr3_nucl(ll,k)=gradxorr3_nucl(ll,k)-gradlongkl + gradxorr3_nucl(ll,l)=gradxorr3_nucl(ll,l)+gradlongkl + enddo + ehbcorr3_nucl=ekont*ees + return + end function ehbcorr3_nucl +#ifdef MPI + subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer) + integer dimen1,dimen2,atom,indx,numcont,i,ii,k,j,num_kont,num_kont_old + real(kind=8):: buffer(dimen1,dimen2) + num_kont=num_cont_hb(atom) + do i=1,num_kont + do k=1,8 + do j=1,3 + buffer(i,indx+(k-1)*3+j)=zapas2(j,i,atom,k) + enddo ! j + enddo ! k + buffer(i,indx+25)=facont_hb(i,atom) + buffer(i,indx+26)=ees0p(i,atom) + buffer(i,indx+27)=ees0m(i,atom) + buffer(i,indx+28)=d_cont(i,atom) + buffer(i,indx+29)=dfloat(jcont_hb(i,atom)) + enddo ! i + buffer(1,indx+30)=dfloat(num_kont) + return + end subroutine pack_buffer +!c------------------------------------------------------------------------------ + subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer) + integer dimen1,dimen2,atom,indx,numcont,i,ii,k,j,num_kont,num_kont_old + real(kind=8):: buffer(dimen1,dimen2) +! double precision zapas +! common /contacts_hb/ zapas(3,maxconts,maxres,8), +! & facont_hb(maxconts,maxres),ees0p(maxconts,maxres), +! & ees0m(maxconts,maxres),d_cont(maxconts,maxres), +! & num_cont_hb(maxres),jcont_hb(maxconts,maxres) + num_kont=buffer(1,indx+30) + num_kont_old=num_cont_hb(atom) + num_cont_hb(atom)=num_kont+num_kont_old + do i=1,num_kont + ii=i+num_kont_old + do k=1,8 + do j=1,3 + zapas2(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j) + enddo ! j + enddo ! k + facont_hb(ii,atom)=buffer(i,indx+25) + ees0p(ii,atom)=buffer(i,indx+26) + ees0m(ii,atom)=buffer(i,indx+27) + d_cont(i,atom)=buffer(i,indx+28) + jcont_hb(ii,atom)=buffer(i,indx+29) + enddo ! i + return + end subroutine unpack_buffer +!c------------------------------------------------------------------------------ +#endif + subroutine ecatcat(ecationcation) + integer :: i,j,itmp,xshift,yshift,zshift,subchap,k + real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,& + r7,r4,ecationcation,k0,rcal + real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, & + dist_init,dist_temp,Evan1cat,Evan2cat,Eeleccat + real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,& + gg,r + + ecationcation=0.0d0 + if (nres_molec(5).eq.0) return + rcat0=3.472 + epscalc=0.05 + r06 = rcat0**6 + r012 = r06**2 + k0 = 332.0*(2.0*2.0)/80.0 + itmp=0 + do i=1,4 + itmp=itmp+nres_molec(i) + enddo + do i=itmp+1,itmp+nres_molec(i)-1 + + xi=c(1,i) + yi=c(2,i) + zi=c(3,i) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + + do j=i+1,itmp+nres_molec(5) +! print *,i,j,'catcat' + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + rcal =xj**2+yj**2+zj**2 + ract=sqrt(rcal) +! rcat0=3.472 +! epscalc=0.05 +! r06 = rcat0**6 +! r012 = r06**2 +! k0 = 332*(2*2)/80 + Evan1cat=epscalc*(r012/rcal**6) + Evan2cat=epscalc*2*(r06/rcal**3) + Eeleccat=k0/ract + r7 = rcal**7 + r4 = rcal**4 + r(1)=xj + r(2)=yj + r(3)=zj + do k=1,3 + dEvan1Cmcat(k)=-12*r(k)*epscalc*r012/r7 + dEvan2Cmcat(k)=-12*r(k)*epscalc*r06/r4 + dEeleccat(k)=-k0*r(k)/ract**3 + enddo + do k=1,3 + gg(k) = dEvan1Cmcat(k)+dEvan2Cmcat(k)+dEeleccat(k) + gradcatcat(k,i)=gradcatcat(k,i)-gg(k) + gradcatcat(k,j)=gradcatcat(k,j)+gg(k) + enddo + + ecationcation=ecationcation+Evan1cat+Evan2cat+Eeleccat + enddo + enddo + return + end subroutine ecatcat +!--------------------------------------------------------------------------- + subroutine ecat_prot(ecation_prot) + integer i,j,k,subchap,itmp,inum + real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,& + r7,r4,ecationcation + real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, & + dist_init,dist_temp,ecation_prot,rcal,rocal, & + Evan1,Evan2,EC,cm1mag,DASGL,delta,r0p,Epepcat, & + catl,cml,calpl, Etotal_p, Etotal_m,rtab,wdip,wmodquad,wquad1, & + wquad2,wvan1,E1,E2,wconst,wvan2,rcpm,dcmag,sin2thet,sinthet, & + costhet,v1m,v2m,wh2o,wc,rsecp,Ir,Irsecp,Irthrp,Irfourp,Irfiftp,& + Irsistp,Irseven,Irtwelv,Irthir,dE1dr,dE2dr,dEdcos,wquad2p,opt, & + rs,rthrp,rfourp,rsixp,reight,Irsixp,Ireight,Irtw,Irfourt, & + opt1,opt2,opt3,opt4,opt5,opt6,opt7,opt8,opt9,opt10,opt11,opt12,& + opt13,opt14,opt15,opt16,opt17,opt18,opt19, & + Equad1,Equad2,dscmag,v1dpv2,dscmag3,constA,constB,Edip + real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,& + gg,r,EtotalCat,dEtotalCm,dEtotalCalp,dEvan1Cm,dEvan2Cm, & + dEtotalpep,dEtotalcat_num,dEddci,dEtotalcm_num,dEtotalcalp_num, & + tab1,tab2,tab3,diff,cm1,sc,p,tcat,talp,cm,drcp,drcp_norm,vcat, & + v1,v2,v3,myd_norm,dx,vcm,valpha,drdpep,dcosdpep,dcosddci,dEdpep,& + dEcCat,dEdipCm,dEdipCalp,dEquad1Cat,dEquad1Cm,dEquad1Calp, & + dEquad2Cat,dEquad2Cm,dEquad2Calpd,Evan1Cat,dEvan1Calp,dEvan2Cat,& + dEvan2Calp,dEtotalCat,dscvec,dEcCm,dEcCalp,dEdipCat,dEquad2Calp,& + dEvan1Cat + real(kind=8),dimension(6) :: vcatprm + ecation_prot=0.0d0 +! first lets calculate interaction with peptide groups + if (nres_molec(5).eq.0) return + wconst=78 + wdip =1.092777950857032D2 + wdip=wdip/wconst + wmodquad=-2.174122713004870D4 + wmodquad=wmodquad/wconst + wquad1 = 3.901232068562804D1 + wquad1=wquad1/wconst + wquad2 = 3 + wquad2=wquad2/wconst + wvan1 = 0.1 + wvan2 = 6 + itmp=0 + do i=1,4 + itmp=itmp+nres_molec(i) + enddo + do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization +! cycle + if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms + xi=0.5d0*(c(1,i)+c(1,i+1)) + yi=0.5d0*(c(2,i)+c(2,i+1)) + zi=0.5d0*(c(3,i)+c(3,i+1)) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + + do j=itmp+1,itmp+nres_molec(5) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif +! enddo +! enddo + rcpm = sqrt(xj**2+yj**2+zj**2) + drcp_norm(1)=xj/rcpm + drcp_norm(2)=yj/rcpm + drcp_norm(3)=zj/rcpm + dcmag=0.0 + do k=1,3 + dcmag=dcmag+dc(k,i)**2 + enddo + dcmag=dsqrt(dcmag) + do k=1,3 + myd_norm(k)=dc(k,i)/dcmag + enddo + costhet=drcp_norm(1)*myd_norm(1)+drcp_norm(2)*myd_norm(2)+& + drcp_norm(3)*myd_norm(3) + rsecp = rcpm**2 + Ir = 1.0d0/rcpm + Irsecp = 1.0d0/rsecp + Irthrp = Irsecp/rcpm + Irfourp = Irthrp/rcpm + Irfiftp = Irfourp/rcpm + Irsistp=Irfiftp/rcpm + Irseven=Irsistp/rcpm + Irtwelv=Irsistp*Irsistp + Irthir=Irtwelv/rcpm + sin2thet = (1-costhet*costhet) + sinthet=sqrt(sin2thet) + E1 = wdip*Irsecp*costhet+(wmodquad*Irfourp+wquad1*Irthrp)& + *sin2thet + E2 = -wquad1*Irthrp*wquad2+wvan1*(wvan2**12*Irtwelv-& + 2*wvan2**6*Irsistp) + ecation_prot = ecation_prot+E1+E2 + dE1dr = -2*costhet*wdip*Irthrp-& + (4*wmodquad*Irfiftp+3*wquad1*Irfourp)*sin2thet + dE2dr = 3*wquad1*wquad2*Irfourp- & + 12*wvan1*wvan2**6*(wvan2**6*Irthir-Irseven) + dEdcos = wdip*Irsecp-2*(wmodquad*Irfourp+wquad1*Irthrp)*costhet + do k=1,3 + drdpep(k) = -drcp_norm(k) + dcosdpep(k) = Ir*(costhet*drcp_norm(k)-myd_norm(k)) + dcosddci(k) = drcp_norm(k)/dcmag-costhet*myd_norm(k)/dcmag + dEdpep(k) = (dE1dr+dE2dr)*drdpep(k)+dEdcos*dcosdpep(k) + dEddci(k) = dEdcos*dcosddci(k) + enddo + do k=1,3 + gradpepcat(k,i)=gradpepcat(k,i)+0.5D0*dEdpep(k)-dEddci(k) + gradpepcat(k,i+1)=gradpepcat(k,i+1)+0.5D0*dEdpep(k)+dEddci(k) + gradpepcat(k,j)=gradpepcat(k,j)-dEdpep(k) + enddo + enddo ! j + enddo ! i +!------------------------------------------sidechains + do i=1,nres_molec(1) + if ((itype(i,1).eq.ntyp1)) cycle ! leave dummy atoms +! cycle +! print *,i,ecation_prot + xi=(c(1,i+nres)) + yi=(c(2,i+nres)) + zi=(c(3,i+nres)) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + do k=1,3 + cm1(k)=dc(k,i+nres) + enddo + cm1mag=sqrt(cm1(1)**2+cm1(2)**2+cm1(3)**2) + do j=itmp+1,itmp+nres_molec(5) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif +! enddo +! enddo + if(itype(i,1).eq.15.or.itype(i,1).eq.16) then + if(itype(i,1).eq.16) then + inum=1 + else + inum=2 + endif + do k=1,6 + vcatprm(k)=catprm(k,inum) + enddo + dASGL=catprm(7,inum) + do k=1,3 + vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres) + valpha(k)=c(k,i) + vcat(k)=c(k,j) + enddo + do k=1,3 + dx(k) = vcat(k)-vcm(k) + enddo + do k=1,3 + v1(k)=(vcm(k)-valpha(k)) + v2(k)=(vcat(k)-valpha(k)) + enddo + v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2) + v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2) + v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3) + +! The weights of the energy function calculated from +!The quantum mechanical GAMESS simulations of calcium with ASP/GLU + wh2o=78 + wc = vcatprm(1) + wc=wc/wh2o + wdip =vcatprm(2) + wdip=wdip/wh2o + wquad1 =vcatprm(3) + wquad1=wquad1/wh2o + wquad2 = vcatprm(4) + wquad2=wquad2/wh2o + wquad2p = 1-wquad2 + wvan1 = vcatprm(5) + wvan2 =vcatprm(6) + opt = dx(1)**2+dx(2)**2 + rsecp = opt+dx(3)**2 + rs = sqrt(rsecp) + rthrp = rsecp*rs + rfourp = rthrp*rs + rsixp = rfourp*rsecp + reight=rsixp*rsecp + Ir = 1.0d0/rs + Irsecp = 1/rsecp + Irthrp = Irsecp/rs + Irfourp = Irthrp/rs + Irsixp = 1/rsixp + Ireight=1/reight + Irtw=Irsixp*Irsixp + Irthir=Irtw/rs + Irfourt=Irthir/rs + opt1 = (4*rs*dx(3)*wdip) + opt2 = 6*rsecp*wquad1*opt + opt3 = wquad1*wquad2p*Irsixp + opt4 = (wvan1*wvan2**12) + opt5 = opt4*12*Irfourt + opt6 = 2*wvan1*wvan2**6 + opt7 = 6*opt6*Ireight + opt8 = wdip/v1m + opt10 = wdip/v2m + opt11 = (rsecp*v2m)**2 + opt12 = (rsecp*v1m)**2 + opt14 = (v1m*v2m*rsecp)**2 + opt15 = -wquad1/v2m**2 + opt16 = (rthrp*(v1m*v2m)**2)**2 + opt17 = (v1m**2*rthrp)**2 + opt18 = -wquad1/rthrp + opt19 = (v1m**2*v2m**2)**2 + Ec = wc*Ir + do k=1,3 + dEcCat(k) = -(dx(k)*wc)*Irthrp + dEcCm(k)=(dx(k)*wc)*Irthrp + dEcCalp(k)=0.0d0 + enddo + Edip=opt8*(v1dpv2)/(rsecp*v2m) + do k=1,3 + dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m & + *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11 + dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m & + *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12 + dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m & + *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp) & + *v1dpv2)/opt14 + enddo + Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2) + do k=1,3 + dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp* & + (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2* & + v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16 + dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp* & + (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2* & + v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16 + dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* & + v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)* & + v1dpv2**2)/opt19 + enddo + Equad2=wquad1*wquad2p*Irthrp + do k=1,3 + dEquad2Cat(k)=-3*dx(k)*rs*opt3 + dEquad2Cm(k)=3*dx(k)*rs*opt3 + dEquad2Calp(k)=0.0d0 + enddo + Evan1=opt4*Irtw + do k=1,3 + dEvan1Cat(k)=-dx(k)*opt5 + dEvan1Cm(k)=dx(k)*opt5 + dEvan1Calp(k)=0.0d0 + enddo + Evan2=-opt6*Irsixp + do k=1,3 + dEvan2Cat(k)=dx(k)*opt7 + dEvan2Cm(k)=-dx(k)*opt7 + dEvan2Calp(k)=0.0d0 + enddo + ecation_prot=ecation_prot+Ec+Edip+Equad1+Equad2+Evan1+Evan2 +! print *,ecation_prot,Ec+Edip+Equad1+Equad2+Evan1+Evan2 + + do k=1,3 + dEtotalCat(k)=dEcCat(k)+dEdipCat(k)+dEquad1Cat(k)+ & + dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k) +!c write(*,*) 'dEtotalCat inside', (dEtotalCat(l),l=1,3) + dEtotalCm(k)=dEcCm(k)+dEdipCm(k)+dEquad1Cm(k)+ & + dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k) + dEtotalCalp(k)=dEcCalp(k)+dEdipCalp(k)+dEquad1Calp(k) & + +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k) + enddo + dscmag = 0.0d0 + do k=1,3 + dscvec(k) = dc(k,i+nres) + dscmag = dscmag+dscvec(k)*dscvec(k) + enddo + dscmag3 = dscmag + dscmag = sqrt(dscmag) + dscmag3 = dscmag3*dscmag + constA = 1.0d0+dASGL/dscmag + constB = 0.0d0 + do k=1,3 + constB = constB+dscvec(k)*dEtotalCm(k) + enddo + constB = constB*dASGL/dscmag3 + do k=1,3 + gg(k) = dEtotalCm(k)+dEtotalCalp(k) + gradpepcatx(k,i)=gradpepcatx(k,i)+ & + constA*dEtotalCm(k)-constB*dscvec(k) +! print *,j,constA,dEtotalCm(k),constB,dscvec(k) + gradpepcat(k,i)=gradpepcat(k,i)+gg(k) + gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k) + enddo + else if (itype(i,1).eq.13.or.itype(i,1).eq.14) then + if(itype(i,1).eq.14) then + inum=3 + else + inum=4 + endif + do k=1,6 + vcatprm(k)=catprm(k,inum) + enddo + dASGL=catprm(7,inum) + do k=1,3 + vcm(k)=(cm1(k)/cm1mag)*dASGL+c(k,i+nres) + valpha(k)=c(k,i) + vcat(k)=c(k,j) + enddo + + do k=1,3 + dx(k) = vcat(k)-vcm(k) + enddo + do k=1,3 + v1(k)=(vcm(k)-valpha(k)) + v2(k)=(vcat(k)-valpha(k)) + enddo + v1m = sqrt(v1(1)**2+v1(2)**2+v1(3)**2) + v2m = sqrt(v2(1)**2+v2(2)**2+v2(3)**2) + v1dpv2 = v1(1)*v2(1)+v1(2)*v2(2)+v1(3)*v2(3) +! The weights of the energy function calculated from +!The quantum mechanical GAMESS simulations of ASN/GLN with calcium + wh2o=78 + wdip =vcatprm(2) + wdip=wdip/wh2o + wquad1 =vcatprm(3) + wquad1=wquad1/wh2o + wquad2 = vcatprm(4) + wquad2=wquad2/wh2o + wquad2p = 1-wquad2 + wvan1 = vcatprm(5) + wvan2 =vcatprm(6) + opt = dx(1)**2+dx(2)**2 + rsecp = opt+dx(3)**2 + rs = sqrt(rsecp) + rthrp = rsecp*rs + rfourp = rthrp*rs + rsixp = rfourp*rsecp + reight=rsixp*rsecp + Ir = 1.0d0/rs + Irsecp = 1/rsecp + Irthrp = Irsecp/rs + Irfourp = Irthrp/rs + Irsixp = 1/rsixp + Ireight=1/reight + Irtw=Irsixp*Irsixp + Irthir=Irtw/rs + Irfourt=Irthir/rs + opt1 = (4*rs*dx(3)*wdip) + opt2 = 6*rsecp*wquad1*opt + opt3 = wquad1*wquad2p*Irsixp + opt4 = (wvan1*wvan2**12) + opt5 = opt4*12*Irfourt + opt6 = 2*wvan1*wvan2**6 + opt7 = 6*opt6*Ireight + opt8 = wdip/v1m + opt10 = wdip/v2m + opt11 = (rsecp*v2m)**2 + opt12 = (rsecp*v1m)**2 + opt14 = (v1m*v2m*rsecp)**2 + opt15 = -wquad1/v2m**2 + opt16 = (rthrp*(v1m*v2m)**2)**2 + opt17 = (v1m**2*rthrp)**2 + opt18 = -wquad1/rthrp + opt19 = (v1m**2*v2m**2)**2 + Edip=opt8*(v1dpv2)/(rsecp*v2m) + do k=1,3 + dEdipCat(k)=opt8*(v1(k)*rsecp*v2m-((v2(k)/v2m& + *rsecp+2*dx(k)*v2m)*v1dpv2))/opt11 + dEdipCm(k)=opt10*(v2(k)*rsecp*v1m-((v1(k)/v1m& + *rsecp-2*dx(k)*v1m)*v1dpv2))/opt12 + dEdipCalp(k)=wdip*((-v1(k)-v2(k))*rsecp*v1m& + *v2m-(-v1(k)/v1m*v2m*rsecp-v2(k)/v2m*v1m*rsecp)& + *v1dpv2)/opt14 + enddo + Equad1=-wquad1*v1dpv2**2/(rthrp*(v1m*v2m)**2) + do k=1,3 + dEquad1Cat(k)=-wquad1*(2*v1(k)*v1dpv2*(rthrp*& + (v1m*v2m)**2)-(3*dx(k)*rs*(v1m*v2m)**2+2*v1m*2*& + v2(k)*1/2*1/v2m*v1m*v2m*rthrp)*v1dpv2**2)/opt16 + dEquad1Cm(k)=-wquad1*(2*v2(k)*v1dpv2*(rthrp*& + (v1m*v2m)**2)-(-3*dx(k)*rs*(v1m*v2m)**2+2*v2m*2*& + v1(k)*1/2*1/v1m*v2m*v1m*rthrp)*v1dpv2**2)/opt16 + dEquad1Calp(k)=opt18*(2*(-v1(k)-v2(k))*v1dpv2* & + v1m**2*v2m**2-(-2*v1(k)*v2m**2-2*v2(k)*v1m**2)*& + v1dpv2**2)/opt19 + enddo + Equad2=wquad1*wquad2p*Irthrp + do k=1,3 + dEquad2Cat(k)=-3*dx(k)*rs*opt3 + dEquad2Cm(k)=3*dx(k)*rs*opt3 + dEquad2Calp(k)=0.0d0 + enddo + Evan1=opt4*Irtw + do k=1,3 + dEvan1Cat(k)=-dx(k)*opt5 + dEvan1Cm(k)=dx(k)*opt5 + dEvan1Calp(k)=0.0d0 + enddo + Evan2=-opt6*Irsixp + do k=1,3 + dEvan2Cat(k)=dx(k)*opt7 + dEvan2Cm(k)=-dx(k)*opt7 + dEvan2Calp(k)=0.0d0 + enddo + ecation_prot = ecation_prot+Edip+Equad1+Equad2+Evan1+Evan2 + do k=1,3 + dEtotalCat(k)=dEdipCat(k)+dEquad1Cat(k)+ & + dEquad2Cat(k)+dEvan1Cat(k)+dEvan2Cat(k) + dEtotalCm(k)=dEdipCm(k)+dEquad1Cm(k)+ & + dEquad2Cm(k)+dEvan1Cm(k)+dEvan2Cm(k) + dEtotalCalp(k)=dEdipCalp(k)+dEquad1Calp(k) & + +dEquad2Calp(k)+dEvan1Calp(k)+dEvan2Calp(k) + enddo + dscmag = 0.0d0 + do k=1,3 + dscvec(k) = c(k,i+nres)-c(k,i) + dscmag = dscmag+dscvec(k)*dscvec(k) + enddo + dscmag3 = dscmag + dscmag = sqrt(dscmag) + dscmag3 = dscmag3*dscmag + constA = 1+dASGL/dscmag + constB = 0.0d0 + do k=1,3 + constB = constB+dscvec(k)*dEtotalCm(k) + enddo + constB = constB*dASGL/dscmag3 + do k=1,3 + gg(k) = dEtotalCm(k)+dEtotalCalp(k) + gradpepcatx(k,i)=gradpepcatx(k,i)+ & + constA*dEtotalCm(k)-constB*dscvec(k) + gradpepcat(k,i)=gradpepcat(k,i)+gg(k) + gradpepcat(k,j)=gradpepcat(k,j)+dEtotalCat(k) + enddo + else + rcal = 0.0d0 + do k=1,3 + r(k) = c(k,j)-c(k,i+nres) + rcal = rcal+r(k)*r(k) + enddo + ract=sqrt(rcal) + rocal=1.5 + epscalc=0.2 + r0p=0.5*(rocal+sig0(itype(i,1))) + r06 = r0p**6 + r012 = r06*r06 + Evan1=epscalc*(r012/rcal**6) + Evan2=epscalc*2*(r06/rcal**3) + r4 = rcal**4 + r7 = rcal**7 + do k=1,3 + dEvan1Cm(k) = 12*r(k)*epscalc*r012/r7 + dEvan2Cm(k) = 12*r(k)*epscalc*r06/r4 + enddo + do k=1,3 + dEtotalCm(k)=dEvan1Cm(k)+dEvan2Cm(k) + enddo + ecation_prot = ecation_prot+ Evan1+Evan2 + do k=1,3 + gradpepcatx(k,i)=gradpepcatx(k,i)+ & + dEtotalCm(k) + gradpepcat(k,i)=gradpepcat(k,i)+dEtotalCm(k) + gradpepcat(k,j)=gradpepcat(k,j)-dEtotalCm(k) + enddo + endif ! 13-16 residues + enddo !j + enddo !i + return + end subroutine ecat_prot + +!---------------------------------------------------------------------------- +!----------------------------------------------------------------------------- +!----------------------------------------------------------------------------- + subroutine eprot_sc_base(escbase) + use calc_data +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.GEO' +! include 'COMMON.VAR' +! include 'COMMON.LOCAL' +! include 'COMMON.CHAIN' +! include 'COMMON.DERIV' +! include 'COMMON.NAMES' +! include 'COMMON.INTERACT' +! include 'COMMON.IOUNITS' +! include 'COMMON.CALC' +! include 'COMMON.CONTROL' +! include 'COMMON.SBRIDGE' + logical :: lprn +!el local variables + integer :: iint,itypi,itypi1,itypj,subchap + real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi + real(kind=8) :: evdw,sig0ij + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, & + sslipi,sslipj,faclip + integer :: ii + real(kind=8) :: fracinbuf + real (kind=8) :: escbase + real (kind=8),dimension(4):: ener + real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out + real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,& + sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,& + Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,& + dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,& + r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,& + dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,& + sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1 + real(kind=8),dimension(3,2)::chead,erhead_tail + real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead + integer troll + eps_out=80.0d0 + escbase=0.0d0 +! do i=1,nres_molec(1) + do i=ibond_start,ibond_end + if (itype(i,1).eq.ntyp1_molec(1)) cycle + itypi = itype(i,1) + dxi = dc_norm(1,nres+i) + dyi = dc_norm(2,nres+i) + dzi = dc_norm(3,nres+i) + dsci_inv = vbld_inv(i+nres) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1) + itypj= itype(j,2) + if (itype(j,2).eq.ntyp1_molec(2))cycle + xj=c(1,j+nres) + yj=c(2,j+nres) + zj=c(3,j+nres) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + dxj = dc_norm( 1, nres+j ) + dyj = dc_norm( 2, nres+j ) + dzj = dc_norm( 3, nres+j ) +! print *,i,j,itypi,itypj + d1i = dhead_scbasei(itypi,itypj) !this is shift of dipole/charge + d1j = dhead_scbasej(itypi,itypj) !this is shift of dipole/charge +! d1i=0.0d0 +! d1j=0.0d0 +! BetaT = 1.0d0 / (298.0d0 * Rb) +! Gay-berne var's + sig0ij = sigma_scbase( itypi,itypj ) + chi1 = chi_scbase( itypi, itypj,1 ) + chi2 = chi_scbase( itypi, itypj,2 ) +! chi1=0.0d0 +! chi2=0.0d0 + chi12 = chi1 * chi2 + chip1 = chipp_scbase( itypi, itypj,1 ) + chip2 = chipp_scbase( itypi, itypj,2 ) +! chip1=0.0d0 +! chip2=0.0d0 + chip12 = chip1 * chip2 +! not used by momo potential, but needed by sc_angular which is shared +! by all energy_potential subroutines + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + a12sq = rborn_scbasei(itypi,itypj) * rborn_scbasej(itypi,itypj) +! a12sq = a12sq * a12sq +! charge of amino acid itypi is... + chis1 = chis_scbase(itypi,itypj,1) + chis2 = chis_scbase(itypi,itypj,2) + chis12 = chis1 * chis2 + sig1 = sigmap1_scbase(itypi,itypj) + sig2 = sigmap2_scbase(itypi,itypj) +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig2 = ", sig2 +! alpha factors from Fcav/Gcav + b1 = alphasur_scbase(1,itypi,itypj) +! b1=0.0d0 + b2 = alphasur_scbase(2,itypi,itypj) + b3 = alphasur_scbase(3,itypi,itypj) + b4 = alphasur_scbase(4,itypi,itypj) +! used to determine whether we want to do quadrupole calculations +! used by Fgb + eps_in = epsintab_scbase(itypi,itypj) + if (eps_in.eq.0.0) eps_in=1.0 + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +! write (*,*) "eps_inout_fac = ", eps_inout_fac +!------------------------------------------------------------------- +! tail location and distance calculations + DO k = 1,3 +! location of polar head is computed by taking hydrophobic centre +! and moving by a d1 * dc_norm vector +! see unres publications for very informative images + chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres) + chead(k,2) = c(k, j+nres) + d1j * dc_norm(k, j+nres) +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + Rhead_distance(k) = chead(k,2) - chead(k,1) + END DO +! pitagoras (root of sum of squares) + Rhead = dsqrt( & + (Rhead_distance(1)*Rhead_distance(1)) & + + (Rhead_distance(2)*Rhead_distance(2)) & + + (Rhead_distance(3)*Rhead_distance(3))) +!------------------------------------------------------------------- +! zero everything that should be zero'ed + evdwij = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + Fcav=0.0d0 + eheadtail = 0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + Fcav = 0.0d0 + dFdR = 0.0d0 + dCAVdOM1 = 0.0d0 + dCAVdOM2 = 0.0d0 + dCAVdOM12 = 0.0d0 + dscj_inv = vbld_inv(j+nres) +! print *,i,j,dscj_inv,dsci_inv +! rij holds 1/(distance of Calpha atoms) + rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) + rij = dsqrt(rrij) +!---------------------------- + CALL sc_angular +! this should be in elgrad_init but om's are calculated by sc_angular +! which in turn is used by older potentials +! om = omega, sqom = om^2 + sqom1 = om1 * om1 + sqom2 = om2 * om2 + sqom12 = om12 * om12 + +! now we calculate EGB - Gey-Berne +! It will be summed up in evdwij and saved in evdw + sigsq = 1.0D0 / sigsq + sig = sig0ij * dsqrt(sigsq) +! rij_shift = 1.0D0 / rij - sig + sig0ij + rij_shift = 1.0/rij - sig + sig0ij + IF (rij_shift.le.0.0D0) THEN + evdw = 1.0D20 + RETURN + END IF + sigder = -sig * sigsq + rij_shift = 1.0D0 / rij_shift + fac = rij_shift**expon + c1 = fac * fac * aa_scbase(itypi,itypj) +! c1 = 0.0d0 + c2 = fac * bb_scbase(itypi,itypj) +! c2 = 0.0d0 + evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 ) + eps2der = eps3rt * evdwij + eps3der = eps2rt * evdwij +! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij + evdwij = eps2rt * eps3rt * evdwij + c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 + fac = -expon * (c1 + evdwij) * rij_shift + sigder = fac * sigder +! fac = rij * fac +! Calculate distance derivative + gg(1) = fac + gg(2) = fac + gg(3) = fac +! if (b2.gt.0.0) then + fac = chis1 * sqom1 + chis2 * sqom2 & + - 2.0d0 * chis12 * om1 * om2 * om12 +! we will use pom later in Gcav, so dont mess with it! + pom = 1.0d0 - chis1 * chis2 * sqom12 + Lambf = (1.0d0 - (fac / pom)) + Lambf = dsqrt(Lambf) + sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0) +! write (*,*) "sparrow = ", sparrow + Chif = 1.0d0/rij * sparrow + ChiLambf = Chif * Lambf + eagle = dsqrt(ChiLambf) + bat = ChiLambf ** 11.0d0 + top = b1 * ( eagle + b2 * ChiLambf - b3 ) + bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0) + botsq = bot * bot + Fcav = top / bot +! print *,i,j,Fcav + dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf)) + dbot = 12.0d0 * b4 * bat * Lambf + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow +! dFdR = 0.0d0 +! write (*,*) "dFcav/dR = ", dFdR + dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif)) + dbot = 12.0d0 * b4 * bat * Chif + eagle = Lambf * pom + dFdOM1 = -(chis1 * om1 - chis12 * om2 * om12) / (eagle) + dFdOM2 = -(chis2 * om2 - chis12 * om1 * om12) / (eagle) + dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) & + * (chis2 * om2 * om12 - om1) / (eagle * pom) + + dFdL = ((dtop * bot - top * dbot) / botsq) +! dFdL = 0.0d0 + dCAVdOM1 = dFdL * ( dFdOM1 ) + dCAVdOM2 = dFdL * ( dFdOM2 ) + dCAVdOM12 = dFdL * ( dFdOM12 ) + + ertail(1) = xj*rij + ertail(2) = yj*rij + ertail(3) = zj*rij +! eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 +! eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 +! eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 & +! -2.0D0*alf12*eps3der+sigder*sigsq_om12 +! print *,"EOMY",eom1,eom2,eom12 +! erdxi = scalar( ertail(1), dC_norm(1,i+nres) ) +! erdxj = scalar( ertail(1), dC_norm(1,j+nres) ) +! here dtail=0.0 +! facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres) +! facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres) + DO k = 1, 3 +! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) + pom = ertail(k) +!-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) + gvdwx_scbase(k,i) = gvdwx_scbase(k,i) & + - (( dFdR + gg(k) ) * pom) +! +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & +! +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv +! & - ( dFdR * pom ) + pom = ertail(k) +!-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres)) + gvdwx_scbase(k,j) = gvdwx_scbase(k,j) & + + (( dFdR + gg(k) ) * pom) +! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & +! +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv +!c! & + ( dFdR * pom ) + + gvdwc_scbase(k,i) = gvdwc_scbase(k,i) & + - (( dFdR + gg(k) ) * ertail(k)) +!c! & - ( dFdR * ertail(k)) + + gvdwc_scbase(k,j) = gvdwc_scbase(k,j) & + + (( dFdR + gg(k) ) * ertail(k)) +!c! & + ( dFdR * ertail(k)) + + gg(k) = 0.0d0 +!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) + END DO + +! else + +! endif +!Now dipole-dipole + if (wdipdip_scbase(2,itypi,itypj).gt.0.0d0) then + w1 = wdipdip_scbase(1,itypi,itypj) + w2 = -wdipdip_scbase(3,itypi,itypj)/2.0 + w3 = wdipdip_scbase(2,itypi,itypj) +!c!------------------------------------------------------------------- +!c! ECL + fac = (om12 - 3.0d0 * om1 * om2) + c1 = (w1 / (Rhead**3.0d0)) * fac + c2 = (w2 / Rhead ** 6.0d0) & + * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2)) + c3= (w3/ Rhead ** 6.0d0) & + * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2)) + ECL = c1 - c2 + c3 +!c! write (*,*) "w1 = ", w1 +!c! write (*,*) "w2 = ", w2 +!c! write (*,*) "om1 = ", om1 +!c! write (*,*) "om2 = ", om2 +!c! write (*,*) "om12 = ", om12 +!c! write (*,*) "fac = ", fac +!c! write (*,*) "c1 = ", c1 +!c! write (*,*) "c2 = ", c2 +!c! write (*,*) "Ecl = ", Ecl +!c! write (*,*) "c2_1 = ", (w2 / Rhead ** 6.0d0) +!c! write (*,*) "c2_2 = ", +!c! & (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2)) +!c!------------------------------------------------------------------- +!c! dervative of ECL is GCL... +!c! dECL/dr + c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0) + c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) & + * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2)) + c3= (-6.0d0 * w3) / (Rhead ** 7.0d0) & + * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2)) + dGCLdR = c1 - c2 + c3 +!c! dECL/dom1 + c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0) + c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & + * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 ) + c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2)) + dGCLdOM1 = c1 - c2 + c3 +!c! dECL/dom2 + c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0) + c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & + * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 ) + c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1)) + dGCLdOM2 = c1 - c2 + c3 +!c! dECL/dom12 + c1 = w1 / (Rhead ** 3.0d0) + c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac) + dGCLdOM12 = c1 - c2 + c3 + DO k= 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + END DO + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + erdxj = scalar( erhead(1), dC_norm(1,j+nres) ) + facd1 = d1i * vbld_inv(i+nres) + facd2 = d1j * vbld_inv(j+nres) + DO k = 1, 3 + + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gvdwx_scbase(k,i) = gvdwx_scbase(k,i) & + - dGCLdR * pom + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) + gvdwx_scbase(k,j) = gvdwx_scbase(k,j) & + + dGCLdR * pom + + gvdwc_scbase(k,i) = gvdwc_scbase(k,i) & + - dGCLdR * erhead(k) + gvdwc_scbase(k,j) = gvdwc_scbase(k,j) & + + dGCLdR * erhead(k) + END DO + endif +!now charge with dipole eg. ARG-dG + if (wqdip_scbase(2,itypi,itypj).gt.0.0d0) then + alphapol1 = alphapol_scbase(itypi,itypj) + w1 = wqdip_scbase(1,itypi,itypj) + w2 = wqdip_scbase(2,itypi,itypj) +! w1=0.0d0 +! w2=0.0d0 +! pis = sig0head_scbase(itypi,itypj) +! eps_head = epshead_scbase(itypi,itypj) +!c!------------------------------------------------------------------- +!c! R1 - distance between head of ith side chain and tail of jth sidechain + R1 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances tail is center of side-chain + R1=R1+(c(k,j+nres)-chead(k,1))**2 + END DO +!c! Pitagoras + R1 = dsqrt(R1) + +!c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj) +!c! & +dhead(1,1,itypi,itypj))**2)) +!c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj) +!c! & +dhead(2,1,itypi,itypj))**2)) + +!c!------------------------------------------------------------------- +!c! ecl + sparrow = w1 * om1 + hawk = w2 * (1.0d0 - sqom2) + Ecl = sparrow / Rhead**2.0d0 & + - hawk / Rhead**4.0d0 +!c!------------------------------------------------------------------- +!c! derivative of ecl is Gcl +!c! dF/dr part + dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0 +!c! dF/dom1 + dGCLdOM1 = (w1) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * om2) / (Rhead ** 4.0d0) +!c-------------------------------------------------------------------- +!c Polarization energy +!c Epol + MomoFac1 = (1.0d0 - chi1 * sqom2) + RR1 = R1 * R1 / MomoFac1 + ee1 = exp(-( RR1 / (4.0d0 * a12sq) )) + fgb1 = sqrt( RR1 + a12sq * ee1) +! eps_inout_fac=0.0d0 + epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0) +! derivative of Epol is Gpol... + dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) & + / (fgb1 ** 5.0d0) + dFGBdR1 = ( (R1 / MomoFac1) & + * ( 2.0d0 - (0.5d0 * ee1) ) ) & + / ( 2.0d0 * fgb1 ) + dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & + * (2.0d0 - 0.5d0 * ee1) ) & + / (2.0d0 * fgb1) + dPOLdR1 = dPOLdFGB1 * dFGBdR1 +! dPOLdR1 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,1) = ((c(k,j+nres)-chead(k,1))/R1) + END DO + + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + erdxj = scalar( erhead(1), dC_norm(1,j+nres) ) + bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) ) +! bat=0.0d0 + federmaus = scalar(erhead_tail(1,1),dC_norm(1,j+nres)) + facd1 = d1i * vbld_inv(i+nres) + facd2 = d1j * vbld_inv(j+nres) +! facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres) + + DO k = 1, 3 + hawk = (erhead_tail(k,1) + & + facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) +! facd1=0.0d0 +! facd2=0.0d0 + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gvdwx_scbase(k,i) = gvdwx_scbase(k,i) & + - dGCLdR * pom & + - dPOLdR1 * (erhead_tail(k,1)) +! & - dGLJdR * pom + + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) + gvdwx_scbase(k,j) = gvdwx_scbase(k,j) & + + dGCLdR * pom & + + dPOLdR1 * (erhead_tail(k,1)) +! & + dGLJdR * pom + + + gvdwc_scbase(k,i) = gvdwc_scbase(k,i) & + - dGCLdR * erhead(k) & + - dPOLdR1 * erhead_tail(k,1) +! & - dGLJdR * erhead(k) + + gvdwc_scbase(k,j) = gvdwc_scbase(k,j) & + + dGCLdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1) +! & + dGLJdR * erhead(k) + + END DO + endif +! print *,i,j,evdwij,epol,Fcav,ECL + escbase=escbase+evdwij+epol+Fcav+ECL + call sc_grad_scbase + enddo + enddo + + return + end subroutine eprot_sc_base + SUBROUTINE sc_grad_scbase + use calc_data + + real (kind=8) :: dcosom1(3),dcosom2(3) + eom1 = & + eps2der * eps2rt_om1 & + - 2.0D0 * alf1 * eps3der & + + sigder * sigsq_om1 & + + dCAVdOM1 & + + dGCLdOM1 & + + dPOLdOM1 + + eom2 = & + eps2der * eps2rt_om2 & + + 2.0D0 * alf2 * eps3der & + + sigder * sigsq_om2 & + + dCAVdOM2 & + + dGCLdOM2 & + + dPOLdOM2 + + eom12 = & + evdwij * eps1_om12 & + + eps2der * eps2rt_om12 & + - 2.0D0 * alf12 * eps3der & + + sigder *sigsq_om12 & + + dCAVdOM12 & + + dGCLdOM12 + +! print *,eom1,eom2,eom12,i,j,"eom1,2,12",erij(1),erij(2),erij(3) +! print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),& +! gg(1),gg(2),"rozne" + DO k = 1, 3 + dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k)) + dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k)) + gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k) + gvdwx_scbase(k,i)= gvdwx_scbase(k,i) - gg(k) & + + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & + + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv + gvdwx_scbase(k,j)= gvdwx_scbase(k,j) + gg(k) & + + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & + + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + gvdwc_scbase(k,i)=gvdwc_scbase(k,i)-gg(k) + gvdwc_scbase(k,j)=gvdwc_scbase(k,j)+gg(k) + END DO + RETURN + END SUBROUTINE sc_grad_scbase + + + subroutine epep_sc_base(epepbase) + use calc_data + logical :: lprn +!el local variables + integer :: iint,itypi,itypi1,itypj,subchap + real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi + real(kind=8) :: evdw,sig0ij + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, & + sslipi,sslipj,faclip + integer :: ii + real(kind=8) :: fracinbuf + real (kind=8) :: epepbase + real (kind=8),dimension(4):: ener + real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out + real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,& + sqom1,sqom2,sqom12,c1,c2,c3,pom,Lambf,sparrow,& + Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,& + dFdOM2,w1,w2,w3,dGCLdR,dFdL,dFdOM12,dbot ,& + r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,& + dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,& + sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1 + real(kind=8),dimension(3,2)::chead,erhead_tail + real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead + integer troll + eps_out=80.0d0 + epepbase=0.0d0 +! do i=1,nres_molec(1)-1 + do i=ibond_start,ibond_end + if (itype(i,1).eq.ntyp1_molec(1).or.itype(i+1,1).eq.ntyp1_molec(1)) cycle +!C itypi = itype(i,1) + dxi = dc_norm(1,i) + dyi = dc_norm(2,i) + dzi = dc_norm(3,i) +! print *,dxi,(-c(1,i)+c(1,i+1))*vbld_inv(i+1) + dsci_inv = vbld_inv(i+1)/2.0 + xi=(c(1,i)+c(1,i+1))/2.0 + yi=(c(2,i)+c(2,i+1))/2.0 + zi=(c(3,i)+c(3,i+1))/2.0 + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1) + itypj= itype(j,2) + if (itype(j,2).eq.ntyp1_molec(2))cycle + xj=c(1,j+nres) + yj=c(2,j+nres) + zj=c(3,j+nres) + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + xj=xj_safe+xshift*boxxsize + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + dxj = dc_norm( 1, nres+j ) + dyj = dc_norm( 2, nres+j ) + dzj = dc_norm( 3, nres+j ) +! d1i = dhead_scbasei(itypi) !this is shift of dipole/charge +! d1j = dhead_scbasej(itypi) !this is shift of dipole/charge + +! Gay-berne var's + sig0ij = sigma_pepbase(itypj ) + chi1 = chi_pepbase(itypj,1 ) + chi2 = chi_pepbase(itypj,2 ) +! chi1=0.0d0 +! chi2=0.0d0 + chi12 = chi1 * chi2 + chip1 = chipp_pepbase(itypj,1 ) + chip2 = chipp_pepbase(itypj,2 ) +! chip1=0.0d0 +! chip2=0.0d0 + chip12 = chip1 * chip2 + chis1 = chis_pepbase(itypj,1) + chis2 = chis_pepbase(itypj,2) + chis12 = chis1 * chis2 + sig1 = sigmap1_pepbase(itypj) + sig2 = sigmap2_pepbase(itypj) +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig2 = ", sig2 + DO k = 1,3 +! location of polar head is computed by taking hydrophobic centre +! and moving by a d1 * dc_norm vector +! see unres publications for very informative images + chead(k,1) = (c(k,i)+c(k,i+1))/2.0 +! + d1i * dc_norm(k, i+nres) + chead(k,2) = c(k, j+nres) +! + d1j * dc_norm(k, j+nres) +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + Rhead_distance(k) = chead(k,2) - chead(k,1) +! print *,gvdwc_pepbase(k,i) + + END DO + Rhead = dsqrt( & + (Rhead_distance(1)*Rhead_distance(1)) & + + (Rhead_distance(2)*Rhead_distance(2)) & + + (Rhead_distance(3)*Rhead_distance(3))) + +! alpha factors from Fcav/Gcav + b1 = alphasur_pepbase(1,itypj) +! b1=0.0d0 + b2 = alphasur_pepbase(2,itypj) + b3 = alphasur_pepbase(3,itypj) + b4 = alphasur_pepbase(4,itypj) + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) +! print *,i,j,rrij + rij = dsqrt(rrij) +!---------------------------- + evdwij = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + Fcav=0.0d0 + eheadtail = 0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + Fcav = 0.0d0 + dFdR = 0.0d0 + dCAVdOM1 = 0.0d0 + dCAVdOM2 = 0.0d0 + dCAVdOM12 = 0.0d0 + dscj_inv = vbld_inv(j+nres) + CALL sc_angular +! this should be in elgrad_init but om's are calculated by sc_angular +! which in turn is used by older potentials +! om = omega, sqom = om^2 + sqom1 = om1 * om1 + sqom2 = om2 * om2 + sqom12 = om12 * om12 + +! now we calculate EGB - Gey-Berne +! It will be summed up in evdwij and saved in evdw + sigsq = 1.0D0 / sigsq + sig = sig0ij * dsqrt(sigsq) + rij_shift = 1.0/rij - sig + sig0ij + IF (rij_shift.le.0.0D0) THEN + evdw = 1.0D20 + RETURN + END IF + sigder = -sig * sigsq + rij_shift = 1.0D0 / rij_shift + fac = rij_shift**expon + c1 = fac * fac * aa_pepbase(itypj) +! c1 = 0.0d0 + c2 = fac * bb_pepbase(itypj) +! c2 = 0.0d0 + evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 ) + eps2der = eps3rt * evdwij + eps3der = eps2rt * evdwij +! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij + evdwij = eps2rt * eps3rt * evdwij + c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 + fac = -expon * (c1 + evdwij) * rij_shift + sigder = fac * sigder +! fac = rij * fac +! Calculate distance derivative + gg(1) = fac + gg(2) = fac + gg(3) = fac + fac = chis1 * sqom1 + chis2 * sqom2 & + - 2.0d0 * chis12 * om1 * om2 * om12 +! we will use pom later in Gcav, so dont mess with it! + pom = 1.0d0 - chis1 * chis2 * sqom12 + Lambf = (1.0d0 - (fac / pom)) + Lambf = dsqrt(Lambf) + sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0) +! write (*,*) "sparrow = ", sparrow + Chif = 1.0d0/rij * sparrow + ChiLambf = Chif * Lambf + eagle = dsqrt(ChiLambf) + bat = ChiLambf ** 11.0d0 + top = b1 * ( eagle + b2 * ChiLambf - b3 ) + bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0) + botsq = bot * bot + Fcav = top / bot +! print *,i,j,Fcav + dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf)) + dbot = 12.0d0 * b4 * bat * Lambf + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow +! dFdR = 0.0d0 +! write (*,*) "dFcav/dR = ", dFdR + dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif)) + dbot = 12.0d0 * b4 * bat * Chif + eagle = Lambf * pom + dFdOM1 = -(chis1 * om1 - chis12 * om2 * om12) / (eagle) + dFdOM2 = -(chis2 * om2 - chis12 * om1 * om12) / (eagle) + dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) & + * (chis2 * om2 * om12 - om1) / (eagle * pom) + + dFdL = ((dtop * bot - top * dbot) / botsq) +! dFdL = 0.0d0 + dCAVdOM1 = dFdL * ( dFdOM1 ) + dCAVdOM2 = dFdL * ( dFdOM2 ) + dCAVdOM12 = dFdL * ( dFdOM12 ) + + ertail(1) = xj*rij + ertail(2) = yj*rij + ertail(3) = zj*rij + DO k = 1, 3 +! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) + pom = ertail(k) +!-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) + gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) & + - (( dFdR + gg(k) ) * pom)/2.0 +! print *,gvdwc_pepbase(k,i),i,(( dFdR + gg(k) ) * pom)/2.0 +! +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & +! +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv +! & - ( dFdR * pom ) + pom = ertail(k) +!-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres)) + gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) & + + (( dFdR + gg(k) ) * pom) +! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & +! +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv +!c! & + ( dFdR * pom ) + + gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) & + - (( dFdR + gg(k) ) * ertail(k))/2.0 +! print *,gvdwc_pepbase(k,i+1),i+1,(( dFdR + gg(k) ) * pom)/2.0 + +!c! & - ( dFdR * ertail(k)) + + gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) & + + (( dFdR + gg(k) ) * ertail(k)) +!c! & + ( dFdR * ertail(k)) + + gg(k) = 0.0d0 +!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) + END DO + + + w1 = wdipdip_pepbase(1,itypj) + w2 = -wdipdip_pepbase(3,itypj)/2.0 + w3 = wdipdip_pepbase(2,itypj) +! w1=0.0d0 +! w2=0.0d0 +!c!------------------------------------------------------------------- +!c! ECL +! w3=0.0d0 + fac = (om12 - 3.0d0 * om1 * om2) + c1 = (w1 / (Rhead**3.0d0)) * fac + c2 = (w2 / Rhead ** 6.0d0) & + * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2)) + c3= (w3/ Rhead ** 6.0d0) & + * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2)) + + ECL = c1 - c2 + c3 + + c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0) + c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) & + * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2)) + c3= (-6.0d0 * w3) / (Rhead ** 7.0d0) & + * (2.0d0 - 2.0d0*fac*fac +3.0d0*(sqom1 + sqom2)) + + dGCLdR = c1 - c2 + c3 +!c! dECL/dom1 + c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0) + c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & + * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 ) + c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om1-2.0d0*(fac)*(-om2)) + dGCLdOM1 = c1 - c2 + c3 +!c! dECL/dom2 + c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0) + c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & + * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 ) + c3 =(6.0d0*w3/ Rhead ** 6.0d0)*(om2-2.0d0*(fac)*(-om1)) + + dGCLdOM2 = c1 - c2 + c3 +!c! dECL/dom12 + c1 = w1 / (Rhead ** 3.0d0) + c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + c3 = (w3/ Rhead ** 6.0d0)*(-4.0d0*fac) + dGCLdOM12 = c1 - c2 + c3 + DO k= 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + END DO + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + erdxj = scalar( erhead(1), dC_norm(1,j+nres) ) +! facd1 = d1 * vbld_inv(i+nres) +! facd2 = d2 * vbld_inv(j+nres) + DO k = 1, 3 + +! pom = erhead(k) +!+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) +! gvdwx_pepbase(k,i) = gvdwx_scbase(k,i) & +! - dGCLdR * pom + pom = erhead(k) +!+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) + gvdwx_pepbase(k,j) = gvdwx_pepbase(k,j) & + + dGCLdR * pom + + gvdwc_pepbase(k,i) = gvdwc_pepbase(k,i) & + - dGCLdR * erhead(k)/2.0d0 +! print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0 + gvdwc_pepbase(k,i+1) = gvdwc_pepbase(k,i+1) & + - dGCLdR * erhead(k)/2.0d0 +! print *,gvdwc_pepbase(k,i+1),i+1,- dGCLdR * erhead(k)/2.0d0 + gvdwc_pepbase(k,j) = gvdwc_pepbase(k,j) & + + dGCLdR * erhead(k) + END DO +! print *,i,j,evdwij,Fcav,ECL,"vdw,cav,ecl" + epepbase=epepbase+evdwij+Fcav+ECL + call sc_grad_pepbase + enddo + enddo + END SUBROUTINE epep_sc_base + SUBROUTINE sc_grad_pepbase + use calc_data + + real (kind=8) :: dcosom1(3),dcosom2(3) + eom1 = & + eps2der * eps2rt_om1 & + - 2.0D0 * alf1 * eps3der & + + sigder * sigsq_om1 & + + dCAVdOM1 & + + dGCLdOM1 & + + dPOLdOM1 + + eom2 = & + eps2der * eps2rt_om2 & + + 2.0D0 * alf2 * eps3der & + + sigder * sigsq_om2 & + + dCAVdOM2 & + + dGCLdOM2 & + + dPOLdOM2 + + eom12 = & + evdwij * eps1_om12 & + + eps2der * eps2rt_om12 & + - 2.0D0 * alf12 * eps3der & + + sigder *sigsq_om12 & + + dCAVdOM12 & + + dGCLdOM12 +! om12=0.0 +! eom12=0.0 +! print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3) +! if (i.eq.30) print *,gvdwc_pepbase(k,i),- gg(k),& +! (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))& +! *dsci_inv*2.0 +! print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),& +! gg(1),gg(2),"rozne" + DO k = 1, 3 + dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k)) + dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k)) + gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k) + gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k)) & + + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))& + *dsci_inv*2.0 & + - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0 + gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k)) & + - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) & + *dsci_inv*2.0 & + + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0 +! print *,eom12,eom2,om12,om2 +!eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),& +! (eom2*(erij(k)-om2*dc_norm(k,nres+j))) + gvdwx_pepbase(k,j)= gvdwx_pepbase(k,j) + gg(k) & + + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))& + + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + gvdwc_pepbase(k,j)=gvdwc_pepbase(k,j)+gg(k) + END DO + RETURN + END SUBROUTINE sc_grad_pepbase + subroutine eprot_sc_phosphate(escpho) + use calc_data +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.GEO' +! include 'COMMON.VAR' +! include 'COMMON.LOCAL' +! include 'COMMON.CHAIN' +! include 'COMMON.DERIV' +! include 'COMMON.NAMES' +! include 'COMMON.INTERACT' +! include 'COMMON.IOUNITS' +! include 'COMMON.CALC' +! include 'COMMON.CONTROL' +! include 'COMMON.SBRIDGE' + logical :: lprn +!el local variables + integer :: iint,itypi,itypi1,itypj,subchap + real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi + real(kind=8) :: evdw,sig0ij + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, & + sslipi,sslipj,faclip + integer :: ii + real(kind=8) :: fracinbuf + real (kind=8) :: escpho + real (kind=8),dimension(4):: ener + real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out + real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,& + sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,& + Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,& + dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,& + r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,& + dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,& + sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1 + real(kind=8),dimension(3,2)::chead,erhead_tail + real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead + integer troll + eps_out=80.0d0 + escpho=0.0d0 +! do i=1,nres_molec(1) + do i=ibond_start,ibond_end + if (itype(i,1).eq.ntyp1_molec(1)) cycle + itypi = itype(i,1) + dxi = dc_norm(1,nres+i) + dyi = dc_norm(2,nres+i) + dzi = dc_norm(3,nres+i) + dsci_inv = vbld_inv(i+nres) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1 + itypj= itype(j,2) + if ((itype(j,2).eq.ntyp1_molec(2)).or.& + (itype(j+1,2).eq.ntyp1_molec(2))) cycle + xj=(c(1,j)+c(1,j+1))/2.0 + yj=(c(2,j)+c(2,j+1))/2.0 + zj=(c(3,j)+c(3,j+1))/2.0 + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + dxj = dc_norm( 1,j ) + dyj = dc_norm( 2,j ) + dzj = dc_norm( 3,j ) + dscj_inv = vbld_inv(j+1) + +! Gay-berne var's + sig0ij = sigma_scpho(itypi ) + chi1 = chi_scpho(itypi,1 ) + chi2 = chi_scpho(itypi,2 ) +! chi1=0.0d0 +! chi2=0.0d0 + chi12 = chi1 * chi2 + chip1 = chipp_scpho(itypi,1 ) + chip2 = chipp_scpho(itypi,2 ) +! chip1=0.0d0 +! chip2=0.0d0 + chip12 = chip1 * chip2 + chis1 = chis_scpho(itypi,1) + chis2 = chis_scpho(itypi,2) + chis12 = chis1 * chis2 + sig1 = sigmap1_scpho(itypi) + sig2 = sigmap2_scpho(itypi) +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig2 = ", sig2 +! alpha factors from Fcav/Gcav + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + a12sq = rborn_scphoi(itypi) * rborn_scphoj(itypi) + + b1 = alphasur_scpho(1,itypi) +! b1=0.0d0 + b2 = alphasur_scpho(2,itypi) + b3 = alphasur_scpho(3,itypi) + b4 = alphasur_scpho(4,itypi) +! used to determine whether we want to do quadrupole calculations +! used by Fgb + eps_in = epsintab_scpho(itypi) + if (eps_in.eq.0.0) eps_in=1.0 + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +! write (*,*) "eps_inout_fac = ", eps_inout_fac +!------------------------------------------------------------------- +! tail location and distance calculations + d1i = dhead_scphoi(itypi) !this is shift of dipole/charge + d1j = 0.0 + DO k = 1,3 +! location of polar head is computed by taking hydrophobic centre +! and moving by a d1 * dc_norm vector +! see unres publications for very informative images + chead(k,1) = c(k, i+nres) + d1i * dc_norm(k, i+nres) + chead(k,2) = (c(k, j) + c(k, j+1))/2.0 +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + Rhead_distance(k) = chead(k,2) - chead(k,1) + END DO +! pitagoras (root of sum of squares) + Rhead = dsqrt( & + (Rhead_distance(1)*Rhead_distance(1)) & + + (Rhead_distance(2)*Rhead_distance(2)) & + + (Rhead_distance(3)*Rhead_distance(3))) + Rhead_sq=Rhead**2.0 +!------------------------------------------------------------------- +! zero everything that should be zero'ed + evdwij = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + Fcav=0.0d0 + eheadtail = 0.0d0 + dGCLdR=0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + Fcav = 0.0d0 + dFdR = 0.0d0 + dCAVdOM1 = 0.0d0 + dCAVdOM2 = 0.0d0 + dCAVdOM12 = 0.0d0 + dscj_inv = vbld_inv(j+1)/2.0 +!dhead_scbasej(itypi,itypj) +! print *,i,j,dscj_inv,dsci_inv +! rij holds 1/(distance of Calpha atoms) + rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) + rij = dsqrt(rrij) +!---------------------------- + CALL sc_angular +! this should be in elgrad_init but om's are calculated by sc_angular +! which in turn is used by older potentials +! om = omega, sqom = om^2 + sqom1 = om1 * om1 + sqom2 = om2 * om2 + sqom12 = om12 * om12 + +! now we calculate EGB - Gey-Berne +! It will be summed up in evdwij and saved in evdw + sigsq = 1.0D0 / sigsq + sig = sig0ij * dsqrt(sigsq) +! rij_shift = 1.0D0 / rij - sig + sig0ij + rij_shift = 1.0/rij - sig + sig0ij + IF (rij_shift.le.0.0D0) THEN + evdw = 1.0D20 + RETURN + END IF + sigder = -sig * sigsq + rij_shift = 1.0D0 / rij_shift + fac = rij_shift**expon + c1 = fac * fac * aa_scpho(itypi) +! c1 = 0.0d0 + c2 = fac * bb_scpho(itypi) +! c2 = 0.0d0 + evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 ) + eps2der = eps3rt * evdwij + eps3der = eps2rt * evdwij +! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij + evdwij = eps2rt * eps3rt * evdwij + c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 + fac = -expon * (c1 + evdwij) * rij_shift + sigder = fac * sigder +! fac = rij * fac +! Calculate distance derivative + gg(1) = fac + gg(2) = fac + gg(3) = fac + fac = chis1 * sqom1 + chis2 * sqom2 & + - 2.0d0 * chis12 * om1 * om2 * om12 +! we will use pom later in Gcav, so dont mess with it! + pom = 1.0d0 - chis1 * chis2 * sqom12 + Lambf = (1.0d0 - (fac / pom)) + Lambf = dsqrt(Lambf) + sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0) +! write (*,*) "sparrow = ", sparrow + Chif = 1.0d0/rij * sparrow + ChiLambf = Chif * Lambf + eagle = dsqrt(ChiLambf) + bat = ChiLambf ** 11.0d0 + top = b1 * ( eagle + b2 * ChiLambf - b3 ) + bot = 1.0d0 + b4 * (ChiLambf ** 12.0d0) + botsq = bot * bot + Fcav = top / bot + dtop = b1 * ((Lambf / (2.0d0 * eagle)) + (b2 * Lambf)) + dbot = 12.0d0 * b4 * bat * Lambf + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow +! dFdR = 0.0d0 +! write (*,*) "dFcav/dR = ", dFdR + dtop = b1 * ((Chif / (2.0d0 * eagle)) + (b2 * Chif)) + dbot = 12.0d0 * b4 * bat * Chif + eagle = Lambf * pom + dFdOM1 = -(chis1 * om1 - chis12 * om2 * om12) / (eagle) + dFdOM2 = -(chis2 * om2 - chis12 * om1 * om12) / (eagle) + dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) & + * (chis2 * om2 * om12 - om1) / (eagle * pom) + + dFdL = ((dtop * bot - top * dbot) / botsq) +! dFdL = 0.0d0 + dCAVdOM1 = dFdL * ( dFdOM1 ) + dCAVdOM2 = dFdL * ( dFdOM2 ) + dCAVdOM12 = dFdL * ( dFdOM12 ) + + ertail(1) = xj*rij + ertail(2) = yj*rij + ertail(3) = zj*rij + DO k = 1, 3 +! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) +! if (i.eq.3) print *,'decl0',gvdwx_scpho(k,i),i + + pom = ertail(k) +! print *,pom,gg(k),dFdR +!-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) + gvdwx_scpho(k,i) = gvdwx_scpho(k,i) & + - (( dFdR + gg(k) ) * pom) +! +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & +! +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv +! & - ( dFdR * pom ) +! pom = ertail(k) +!-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres)) +! gvdwx_scpho(k,j) = gvdwx_scpho(k,j) & +! + (( dFdR + gg(k) ) * pom) +! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & +! +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv +!c! & + ( dFdR * pom ) + + gvdwc_scpho(k,i) = gvdwc_scpho(k,i) & + - (( dFdR + gg(k) ) * ertail(k)) +!c! & - ( dFdR * ertail(k)) + + gvdwc_scpho(k,j) = gvdwc_scpho(k,j) & + + (( dFdR + gg(k) ) * ertail(k))/2.0 + + gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1) & + + (( dFdR + gg(k) ) * ertail(k))/2.0 + +!c! & + ( dFdR * ertail(k)) + + gg(k) = 0.0d0 + ENDDO +!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) +! alphapol1 = alphapol_scpho(itypi) + if (wqq_scpho(itypi).gt.0.0) then + Qij=wqq_scpho(itypi)/eps_in +! Qij=0.0 + Ecl = (332.0d0 * Qij) / Rhead +!c! derivative of Ecl is Gcl... + dGCLdR = (-332.0d0 * Qij ) / Rhead_sq + else if (wqdip_scpho(2,itypi).gt.0.0d0) then + w1 = wqdip_scpho(1,itypi) + w2 = wqdip_scpho(2,itypi) +! w1=0.0d0 +! w2=0.0d0 +! pis = sig0head_scbase(itypi,itypj) +! eps_head = epshead_scbase(itypi,itypj) +!c!------------------------------------------------------------------- + +!c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj) +!c! & +dhead(1,1,itypi,itypj))**2)) +!c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj) +!c! & +dhead(2,1,itypi,itypj))**2)) + +!c!------------------------------------------------------------------- +!c! ecl + sparrow = w1 * om1 + hawk = w2 * (1.0d0 - sqom2) + Ecl = sparrow / Rhead**2.0d0 & + - hawk / Rhead**4.0d0 +!c!------------------------------------------------------------------- +!c! derivative of ecl is Gcl +!c! dF/dr part + dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0 +!c! dF/dom1 + dGCLdOM1 = (w1) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * om2) / (Rhead ** 4.0d0) + endif + +!c-------------------------------------------------------------------- +!c Polarization energy +!c Epol + R1 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances tail is center of side-chain + R1=R1+((c(k,j)+c(k,j+1))/2.0-chead(k,1))**2 + END DO +!c! Pitagoras + R1 = dsqrt(R1) + + alphapol1 = alphapol_scpho(itypi) +! alphapol1=0.0 + MomoFac1 = (1.0d0 - chi2 * sqom1) + RR1 = R1 * R1 / MomoFac1 + ee1 = exp(-( RR1 / (4.0d0 * a12sq) )) +! print *,"ee1",ee1,a12sq,alphapol1,eps_inout_fac + fgb1 = sqrt( RR1 + a12sq * ee1) +! eps_inout_fac=0.0d0 + epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0) +! derivative of Epol is Gpol... + dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) & + / (fgb1 ** 5.0d0) + dFGBdR1 = ( (R1 / MomoFac1) & + * ( 2.0d0 - (0.5d0 * ee1) ) ) & + / ( 2.0d0 * fgb1 ) + dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & + * (2.0d0 - 0.5d0 * ee1) ) & + / (2.0d0 * fgb1) + dPOLdR1 = dPOLdFGB1 * dFGBdR1 +! dPOLdR1 = 0.0d0 +! dPOLdOM1 = 0.0d0 + dFGBdOM1 = (((R1 * R1 * chi2 * om1) / (MomoFac1 * MomoFac1)) & + * (2.0d0 - 0.5d0 * ee1) ) & + / (2.0d0 * fgb1) + + dPOLdOM1 = dPOLdFGB1 * dFGBdOM1 + dPOLdOM2 = 0.0 + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,1) = (((c(k,j)+c(k,j+1))/2.0-chead(k,1))/R1) + END DO + + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + erdxj = scalar( erhead(1), dC_norm(1,j) ) + bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) ) +! bat=0.0d0 + federmaus = scalar(erhead_tail(1,1),dC_norm(1,j)) + facd1 = d1i * vbld_inv(i+nres) + facd2 = d1j * vbld_inv(j) +! facd4 = dtail(2,itypi,itypj) * vbld_inv(j+nres) + + DO k = 1, 3 + hawk = (erhead_tail(k,1) + & + facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) +! facd1=0.0d0 +! facd2=0.0d0 +! if (i.eq.3) print *,'decl1',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i,& +! pom,(erhead_tail(k,1)) + +! print *,'decl',dGCLdR,dPOLdR1,gvdwc_scpho(k,i) + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gvdwx_scpho(k,i) = gvdwx_scpho(k,i) & + - dGCLdR * pom & + - dPOLdR1 * (erhead_tail(k,1)) +! & - dGLJdR * pom + + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j)) +! gvdwx_scpho(k,j) = gvdwx_scpho(k,j) & +! + dGCLdR * pom & +! + dPOLdR1 * (erhead_tail(k,1)) +! & + dGLJdR * pom + + + gvdwc_scpho(k,i) = gvdwc_scpho(k,i) & + - dGCLdR * erhead(k) & + - dPOLdR1 * erhead_tail(k,1) +! & - dGLJdR * erhead(k) + + gvdwc_scpho(k,j) = gvdwc_scpho(k,j) & + + (dGCLdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1))/2.0 + gvdwc_scpho(k,j+1) = gvdwc_scpho(k,j+1) & + + (dGCLdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1))/2.0 + +! & + dGLJdR * erhead(k) +! if (i.eq.3) print *,'decl2',dGCLdR,dPOLdR1,gvdwc_scpho(k,i),i + + END DO +! if (i.eq.3) print *,i,j,evdwij,epol,Fcav,ECL + escpho=escpho+evdwij+epol+Fcav+ECL + call sc_grad_scpho + enddo + + enddo + + return + end subroutine eprot_sc_phosphate + SUBROUTINE sc_grad_scpho + use calc_data + + real (kind=8) :: dcosom1(3),dcosom2(3) + eom1 = & + eps2der * eps2rt_om1 & + - 2.0D0 * alf1 * eps3der & + + sigder * sigsq_om1 & + + dCAVdOM1 & + + dGCLdOM1 & + + dPOLdOM1 + + eom2 = & + eps2der * eps2rt_om2 & + + 2.0D0 * alf2 * eps3der & + + sigder * sigsq_om2 & + + dCAVdOM2 & + + dGCLdOM2 & + + dPOLdOM2 + + eom12 = & + evdwij * eps1_om12 & + + eps2der * eps2rt_om12 & + - 2.0D0 * alf12 * eps3der & + + sigder *sigsq_om12 & + + dCAVdOM12 & + + dGCLdOM12 +! om12=0.0 +! eom12=0.0 +! print *,eom1,eom2,eom12,om12,i,j,"eom1,2,12",erij(1),erij(2),erij(3) +! if (i.eq.30) print *,gvdwc_scpho(k,i),- gg(k),& +! (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))& +! *dsci_inv*2.0 +! print *,dsci_inv,dscj_inv,dc_norm(2,nres+j),dc_norm(2,nres+i),& +! gg(1),gg(2),"rozne" + DO k = 1, 3 + dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k)) + dcosom2(k) = rij * (dc_norm(k,j) - om2 * erij(k)) + gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k) + gvdwc_scpho(k,j)= gvdwc_scpho(k,j) +0.5*( gg(k)) & + + (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)))& + *dscj_inv*2.0 & + - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0 + gvdwc_scpho(k,j+1)= gvdwc_scpho(k,j+1) +0.5*( gg(k)) & + - (-eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j))) & + *dscj_inv*2.0 & + + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0 + gvdwx_scpho(k,i)= gvdwx_scpho(k,i) - gg(k) & + + (eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) & + + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv + +! print *,eom12,eom2,om12,om2 +!eom12*(-dc_norm(k,i)/2.0-om12*dc_norm(k,nres+j)),& +! (eom2*(erij(k)-om2*dc_norm(k,nres+j))) +! gvdwx_scpho(k,j)= gvdwx_scpho(k,j) + gg(k) & +! + (eom12*(dc_norm(k,i)-om12*dc_norm(k,nres+j))& +! + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + gvdwc_scpho(k,i)=gvdwc_scpho(k,i)-gg(k) + END DO + RETURN + END SUBROUTINE sc_grad_scpho + subroutine eprot_pep_phosphate(epeppho) + use calc_data +! implicit real*8 (a-h,o-z) +! include 'DIMENSIONS' +! include 'COMMON.GEO' +! include 'COMMON.VAR' +! include 'COMMON.LOCAL' +! include 'COMMON.CHAIN' +! include 'COMMON.DERIV' +! include 'COMMON.NAMES' +! include 'COMMON.INTERACT' +! include 'COMMON.IOUNITS' +! include 'COMMON.CALC' +! include 'COMMON.CONTROL' +! include 'COMMON.SBRIDGE' + logical :: lprn +!el local variables + integer :: iint,itypi,itypi1,itypj,subchap + real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,fac,e1,e2,sigm,epsi + real(kind=8) :: evdw,sig0ij + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,aa,bb,ssgradlipi,ssgradlipj, & + sslipi,sslipj,faclip + integer :: ii + real(kind=8) :: fracinbuf + real (kind=8) :: epeppho + real (kind=8),dimension(4):: ener + real(kind=8) :: b1,b2,b3,b4,egb,eps_in,eps_inout_fac,eps_out + real(kind=8) :: ECL,Elj,Equad,Epol,eheadtail,rhead,dGCLOM2,& + sqom1,sqom2,sqom12,c1,c2,pom,Lambf,sparrow,& + Chif,ChiLambf,bat,eagle,top,bot,botsq,Fcav,dtop,dFdR,dFdOM1,& + dFdOM2,w1,w2,dGCLdR,dFdL,dFdOM12,dbot ,& + r1,eps_head,alphapol1,pis,facd2,d2,facd1,d1,erdxj,erdxi,federmaus,& + dPOLdR1,dFGBdOM2,dFGBdR1,dPOLdFGB1,RR1,MomoFac1,hawk,d1i,d1j,& + sig1,sig2,chis12,chis2,ee1,fgb1,a12sq,chis1,Rhead_sq,Qij,dFGBdOM1 + real(kind=8),dimension(3,2)::chead,erhead_tail + real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead + integer troll + real (kind=8) :: dcosom1(3),dcosom2(3) + epeppho=0.0d0 +! do i=1,nres_molec(1) + do i=ibond_start,ibond_end + if (itype(i,1).eq.ntyp1_molec(1)) cycle + itypi = itype(i,1) + dsci_inv = vbld_inv(i+1)/2.0 + dxi = dc_norm(1,i) + dyi = dc_norm(2,i) + dzi = dc_norm(3,i) + xi=(c(1,i)+c(1,i+1))/2.0 + yi=(c(2,i)+c(2,i+1))/2.0 + zi=(c(3,i)+c(3,i+1))/2.0 + xi=mod(xi,boxxsize) + if (xi.lt.0) xi=xi+boxxsize + yi=mod(yi,boxysize) + if (yi.lt.0) yi=yi+boxysize + zi=mod(zi,boxzsize) + if (zi.lt.0) zi=zi+boxzsize + do j=nres_molec(1)+1,nres_molec(2)+nres_molec(1)-1 + itypj= itype(j,2) + if ((itype(j,2).eq.ntyp1_molec(2)).or.& + (itype(j+1,2).eq.ntyp1_molec(2))) cycle + xj=(c(1,j)+c(1,j+1))/2.0 + yj=(c(2,j)+c(2,j+1))/2.0 + zj=(c(3,j)+c(3,j+1))/2.0 + xj=dmod(xj,boxxsize) + if (xj.lt.0) xj=xj+boxxsize + yj=dmod(yj,boxysize) + if (yj.lt.0) yj=yj+boxysize + zj=dmod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + xj_safe=xj + yj_safe=yj + zj_safe=zj + subchap=0 + do xshift=-1,1 + do yshift=-1,1 + do zshift=-1,1 + yj=yj_safe+yshift*boxysize + zj=zj_safe+zshift*boxzsize + dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + if(dist_temp.lt.dist_init) then + dist_init=dist_temp + xj_temp=xj + yj_temp=yj + zj_temp=zj + subchap=1 + endif + enddo + enddo + enddo + if (subchap.eq.1) then + xj=xj_temp-xi + yj=yj_temp-yi + zj=zj_temp-zi + else + xj=xj_safe-xi + yj=yj_safe-yi + zj=zj_safe-zi + endif + rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) + rij = dsqrt(rrij) + dxj = dc_norm( 1,j ) + dyj = dc_norm( 2,j ) + dzj = dc_norm( 3,j ) + dscj_inv = vbld_inv(j+1)/2.0 +! Gay-berne var's + sig0ij = sigma_peppho + chi1=0.0d0 + chi2=0.0d0 + chi12 = chi1 * chi2 + chip1=0.0d0 + chip2=0.0d0 + chip12 = chip1 * chip2 + chis1 = 0.0d0 + chis2 = 0.0d0 + chis12 = chis1 * chis2 + sig1 = sigmap1_peppho + sig2 = sigmap2_peppho +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig1 = ", sig1 +! write (*,*) "sig2 = ", sig2 +! alpha factors from Fcav/Gcav + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + b1 = alphasur_peppho(1) +! b1=0.0d0 + b2 = alphasur_peppho(2) + b3 = alphasur_peppho(3) + b4 = alphasur_peppho(4) + CALL sc_angular + sqom1=om1*om1 + evdwij = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + Fcav=0.0d0 + eheadtail = 0.0d0 + dGCLdR=0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + Fcav = 0.0d0 + dFdR = 0.0d0 + dCAVdOM1 = 0.0d0 + dCAVdOM2 = 0.0d0 + dCAVdOM12 = 0.0d0 + rij_shift = rij + fac = rij_shift**expon + c1 = fac * fac * aa_peppho +! c1 = 0.0d0 + c2 = fac * bb_peppho +! c2 = 0.0d0 + evdwij = c1 + c2 +! Now cavity.................... + eagle = dsqrt(1.0/rij_shift) + top = b1 * ( eagle + b2 * 1.0/rij_shift - b3 ) + bot = 1.0d0 + b4 * (1.0/rij_shift ** 12.0d0) + botsq = bot * bot + Fcav = top / bot + dtop = b1 * ((1.0/ (2.0d0 * eagle)) + (b2)) + dbot = 12.0d0 * b4 * (1.0/rij_shift) ** 11.0d0 + dFdR = ((dtop * bot - top * dbot) / botsq) + w1 = wqdip_peppho(1) + w2 = wqdip_peppho(2) +! w1=0.0d0 +! w2=0.0d0 +! pis = sig0head_scbase(itypi,itypj) +! eps_head = epshead_scbase(itypi,itypj) +!c!------------------------------------------------------------------- + +!c! R1 = dsqrt((Rtail**2)+((dtail(1,itypi,itypj) +!c! & +dhead(1,1,itypi,itypj))**2)) +!c! R2 = dsqrt((Rtail**2)+((dtail(2,itypi,itypj) +!c! & +dhead(2,1,itypi,itypj))**2)) + +!c!------------------------------------------------------------------- +!c! ecl + sparrow = w1 * om1 + hawk = w2 * (1.0d0 - sqom1) + Ecl = sparrow * rij_shift**2.0d0 & + - hawk * rij_shift**4.0d0 +!c!------------------------------------------------------------------- +!c! derivative of ecl is Gcl +!c! dF/dr part +! rij_shift=5.0 + dGCLdR = - 2.0d0 * sparrow * rij_shift**3.0d0 & + + 4.0d0 * hawk * rij_shift**5.0d0 +!c! dF/dom1 + dGCLdOM1 = (w1) * (rij_shift**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * om1) * (rij_shift ** 4.0d0) + eom1 = dGCLdOM1+dGCLdOM2 + eom2 = 0.0 + + fac = -expon * (c1 + evdwij) * rij_shift+dFdR+dGCLdR +! fac=0.0 + gg(1) = fac*xj*rij + gg(2) = fac*yj*rij + gg(3) = fac*zj*rij + do k=1,3 + gvdwc_peppho(k,j) = gvdwc_peppho(k,j) +gg(k)/2.0 + gvdwc_peppho(k,j+1) = gvdwc_peppho(k,j+1) +gg(k)/2.0 + gvdwc_peppho(k,i) = gvdwc_peppho(k,i) -gg(k)/2.0 + gvdwc_peppho(k,i+1) = gvdwc_peppho(k,i+1) -gg(k)/2.0 + gg(k)=0.0 + enddo + + DO k = 1, 3 + dcosom1(k) = rij* (dc_norm(k,i) - om1 * erij(k)) + dcosom2(k) = rij* (dc_norm(k,j) - om2 * erij(k)) + gg(k) = gg(k) + eom1 * dcosom1(k)! + eom2 * dcosom2(k) + gvdwc_peppho(k,j)= gvdwc_peppho(k,j) +0.5*( gg(k)) !& +! - (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0 + gvdwc_peppho(k,j+1)= gvdwc_peppho(k,j+1) +0.5*( gg(k)) !& +! + (eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv*2.0 + gvdwc_peppho(k,i)= gvdwc_peppho(k,i) -0.5*( gg(k)) & + - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0 + gvdwc_peppho(k,i+1)= gvdwc_peppho(k,i+1) - 0.5*( gg(k)) & + + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0 + enddo + epeppho=epeppho+evdwij+Fcav+ECL +! print *,i,j,evdwij,Fcav,ECL,rij_shift + enddo + enddo + end subroutine eprot_pep_phosphate end module energy