X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fenergy.F90;h=bb7d08d5afe704eb0f2bd1c4bc4afffc7d5f22aa;hb=refs%2Fheads%2FUCGM;hp=ddc9833cd43ff65c32bf3957f2752600f8acda9e;hpb=bc23440fbe68672d430f71f22f46b11265f003db;p=unres4.git diff --git a/source/unres/energy.F90 b/source/unres/energy.F90 index ddc9833..bb7d08d 100644 --- a/source/unres/energy.F90 +++ b/source/unres/energy.F90 @@ -137,9 +137,12 @@ gvdwc_peppho !------------------------------IONS GRADIENT real(kind=8),dimension(:,:),allocatable :: gradcatcat, & - gradpepcat,gradpepcatx,gradnuclcat,gradnuclcatx + gradpepcat,gradpepcatx,gradnuclcat,gradnuclcatx,gradcattranx,& + gradcattranc,gradcatangc,gradcatangx ! real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2) - +!---------------------------------------- + real(kind=8),dimension(:,:),allocatable ::gradlipelec,gradlipbond,& + gradlipang,gradliplj,gradpepmart, gradpepmartx real(kind=8),dimension(:,:),allocatable :: gel_loc,gel_loc_long,& gcorr3_turn,gcorr4_turn,gcorr6_turn,gradb,gradbx !(3,maxres) @@ -182,7 +185,7 @@ !----------------------------------------------------------------------------- ! common.sbridge ! common /dyn_ssbond/ - real(kind=8),dimension(:,:),allocatable :: dyn_ssbond_ij !(maxres,maxres) + real(kind=8),dimension(:),allocatable :: dyn_ssbond_ij !(maxres,maxres) !----------------------------------------------------------------------------- ! common.sccor ! Parameters of the SCCOR term @@ -198,7 +201,11 @@ ! common /przechowalnia/ real(kind=8),dimension(:,:,:),allocatable :: zapas real(kind=8),dimension(:,:,:,:),allocatable ::zapas2 !(max_dim,maxconts,max_fg_procs) +#ifdef FIVEDIAG + real(kind=8),dimension(:,:),allocatable :: fromto !(3,3,maxdim)(maxdim=(maxres-1)*(maxres-2)/2) +#else real(kind=8),dimension(:,:,:),allocatable :: fromto !(3,3,maxdim)(maxdim=(maxres-1)*(maxres-2)/2) +#endif !----------------------------------------------------------------------------- !----------------------------------------------------------------------------- ! @@ -209,7 +216,7 @@ ! energy_p_new_barrier.F !----------------------------------------------------------------------------- subroutine etotal(energia) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' use MD_data #ifndef ISNAN @@ -248,25 +255,29 @@ ecorr3_nucl ! energies for ions real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,& - ecation_nucl + ecation_nucl,ecat_prottran,ecation_protang ! energies for protein nucleic acid interaction real(kind=8) :: escbase,epepbase,escpho,epeppho +! energies for MARTINI + real(kind=8) :: elipbond,elipang,elipelec,eliplj,elipidprot #ifdef MPI real(kind=8) :: weights_(n_ene) !,time_Bcast,time_Bcastw ! shielding effect varibles for MPI - real(kind=8) :: fac_shieldbuf(nres), & - grad_shield_locbuf1(3*maxcontsshi*nres), & - grad_shield_sidebuf1(3*maxcontsshi*nres), & - grad_shield_locbuf2(3*maxcontsshi*nres), & - grad_shield_sidebuf2(3*maxcontsshi*nres), & - grad_shieldbuf1(3*nres), & - grad_shieldbuf2(3*nres) - - integer ishield_listbuf(-1:nres), & - shield_listbuf(maxcontsshi,-1:nres),k,j,i,iii,impishi,mojint,jjj + real(kind=8) :: fac_shieldbuf(nres_molec(1)), & + grad_shield_locbuf1(3*maxcontsshi*nres_molec(1)), & + grad_shield_sidebuf1(3*maxcontsshi*nres_molec(1)), & + grad_shield_locbuf2(3*maxcontsshi*nres_molec(1)), & + grad_shield_sidebuf2(3*maxcontsshi*nres_molec(1)), & + grad_shieldbuf1(3*nres_molec(1)), & + grad_shieldbuf2(3*nres_molec(1)) + + integer ishield_listbuf(-1:nres_molec(1)), & + shield_listbuf(maxcontsshi,-1:nres_molec(1)),k,j,i,iii,impishi,mojint,jjj + integer :: imatupdate2 ! print *,"I START ENERGY" imatupdate=100 + imatupdate2=100 ! if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list ! real(kind=8), dimension(:),allocatable:: fac_shieldbuf ! real(kind=8), dimension(:,:,:),allocatable:: & @@ -335,6 +346,9 @@ weights_(48)=wscpho weights_(49)=wpeppho weights_(50)=wcatnucl + weights_(56)=wcat_tran + weights_(58)=wlip_prot + weights_(52)=wmartini ! wcatcat= weights(41) ! wcatprot=weights(42) @@ -384,6 +398,9 @@ wscpho=weights(48) wpeppho=weights(49) wcatnucl=weights(50) + wmartini=weights(52) + wcat_tran=weights(56) + wlip_prot=weights(58) ! welpsb=weights(28)*fact(1) ! ! wcorr_nucl= weights(37)*fact(1) @@ -405,8 +422,25 @@ ! write (iout,*) "after make_SCp_inter_list" if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list ! write (iout,*) "after make_SCSC_inter_list" - + if (nres_molec(4).gt.0) then + if (mod(itime_mat,imatupdate).eq.0) call make_lip_pep_list + endif if (mod(itime_mat,imatupdate).eq.0) call make_pp_inter_list + if (nres_molec(5).gt.0) then + if (mod(itime_mat,imatupdate).eq.0) then +! print *,'Processor',myrank,' calling etotal ipot=',ipot + call make_cat_pep_list +! call make_cat_cat_list + endif + endif + endif + if (nres_molec(5).gt.0) then + if (mod(itime_mat,imatupdate2).eq.0) then +! print *, "before cat cat" +! print *,'Processor',myrank,' calling etotal ipot=',ipot +! call make_cat_pep_list + call make_cat_cat_list + endif endif ! write (iout,*) "after make_pp_inter_list" @@ -424,6 +458,7 @@ ! Compute the side-chain and electrostatic interaction energy ! print *, "Before EVDW" ! goto (101,102,103,104,105,106) ipot + if (nres_molec(1).gt.0) then select case(ipot) ! Lennard-Jones potential. ! 101 call elj(evdw) @@ -671,7 +706,7 @@ call escp_soft_sphere(evdw2,evdw2_14) endif ! write(iout,*) "in etotal before ebond",ipot - +! print *,"after escp" ! ! Calculate the bond-stretching energy ! @@ -683,7 +718,7 @@ ! Calculate the disulfide-bridge and other energy and the contributions ! from other distance constraints. ! print *,'Calling EHPB' - call edis(ehpb) +! call edis(ehpb) !elwrite(iout,*) "in etotal afer edis",ipot ! print *,'EHPB exitted succesfully.' ! @@ -708,6 +743,7 @@ ebe=0.0d0 endif ethetacnstr=0.0d0 +! write(iout,*) with_theta_constr,"with_theta_constr" if (with_theta_constr) call etheta_constr(ethetacnstr) ! write(iout,*) "in etotal afer ebe",ipot @@ -717,7 +753,7 @@ ! Calculate the SC local energy. ! call esc(escloc) -!elwrite(iout,*) "in etotal afer esc",ipot +! print *, "in etotal afer esc",wtor ! print *,"Processor",myrank," computed USC" ! ! Calculate the virtual-bond torsional energy. @@ -730,6 +766,7 @@ ! edihcnstr=0 ! endif if (wtor.gt.0.0d0) then +! print *,"WTOR",wtor,tor_mode if (tor_mode.eq.0) then call etor(etors) else @@ -744,6 +781,7 @@ if (ndih_constr.gt.0) call etor_constr(edihcnstr) !c print *,"Processor",myrank," computed Utor" +! print *, "constr_homol",constr_homology ! print *,"Processor",myrank," computed Utor" if (constr_homology.ge.1) then call e_modeller(ehomology_constr) @@ -758,7 +796,7 @@ ! ! 6/23/01 Calculate double-torsional energy ! -!elwrite(iout,*) "in etotal",ipot +! print *, "before etor_d",wtor_d if (wtor_d.gt.0) then call etor_d(etors_d) else @@ -824,6 +862,43 @@ else eliptran=0.0d0 endif + else + eliptran=0.0d0 + evdw=0.0d0 +#ifdef SCP14 + evdw2=0.0d0 + evdw2_14=0.0d0 +#else + evdw2=0.0d0 +#endif +#ifdef SPLITELE + ees=0.0d0 + evdw1=0.0d0 +#else + ees=0.0d0 + evdw1=0.0d0 +#endif + ecorr=0.0d0 + ecorr5=0.0d0 + ecorr6=0.0d0 + eel_loc=0.0d0 + eello_turn3=0.0d0 + eello_turn4=0.0d0 + eturn6=0.0d0 + ebe=0.0d0 + escloc=0.0d0 + etors=0.0d0 + etors_d=0.0d0 + ehpb=0.0d0 + edihcnstr=0.0d0 + estr=0.0d0 + Uconst=0.0d0 + esccor=0.0d0 + ehomology_constr=0.0d0 + ethetacnstr=0.0d0 + endif !nres_molec(1) +! write(iout,*) "TU JEST PRZED EHPB" +! call edis(ehpb) if (fg_rank.eq.0) then if (AFMlog.gt.0) then call AFMforce(Eafmforce) @@ -833,6 +908,7 @@ Eafmforce=0.0d0 endif endif +! print *,"before tubemode",tubemode if (tubemode.eq.1) then call calctube(etube) else if (tubemode.eq.2) then @@ -842,8 +918,11 @@ else etube=0.0d0 endif +! print *, "TU JEST PRZED EHPB" + call edis(ehpb) + !-------------------------------------------------------- -! write (iout,*) "NRES_MOLEC(2),",nres_molec(2) +! print *, "NRES_MOLEC(2),",nres_molec(2) ! print *,"before",ees,evdw1,ecorr ! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2) if (nres_molec(2).gt.0) then @@ -875,22 +954,35 @@ ! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2) ! print *,"before ecatcat",wcatcat if (nres_molec(5).gt.0) then - if (nfgtasks.gt.1) then - if (fg_rank.eq.0) then - call ecatcat(ecationcation) - endif - else - call ecatcat(ecationcation) - endif - if (oldion.gt.0) then - call ecat_prot(ecation_prot) - else - call ecats_prot_amber(ecation_prot) - endif + if (g_ilist_catsctran.gt.0) then + call ecat_prot_transition(ecat_prottran) + else + ecat_prottran=0.0d0 + endif + if (g_ilist_catscang.gt.0) then + call ecat_prot_ang(ecation_protang) + else + ecation_protang=0.0d0 + endif +! if (nfgtasks.gt.1) then +! if (fg_rank.eq.0) then + if (nres_molec(5).gt.1) call ecatcat(ecationcation) +! endif +! else +! if (nres_molec(5).gt.1) call ecatcat(ecationcation) +! endif + if (oldion.gt.0) then + if (g_ilist_catpnorm.gt.0) call ecat_prot(ecation_prot) + else + if (g_ilist_catpnorm.gt.0) call ecats_prot_amber(ecation_prot) + endif else ecationcation=0.0d0 ecation_prot=0.0d0 + ecation_protang=0.0d0 + ecat_prottran=0.0d0 endif + if (g_ilist_catscnorm.eq.0) ecation_prot=0.0d0 if ((nres_molec(2).gt.0).and.(nres_molec(1).gt.0)) then call eprot_sc_base(escbase) call epep_sc_base(epepbase) @@ -902,6 +994,30 @@ escpho=0.0 epeppho=0.0 endif +! MARTINI FORCE FIELD ENERGY TERMS + if (nres_molec(4).gt.0) then + if (nfgtasks.gt.1) then + if (fg_rank.eq.0) then + call lipid_bond(elipbond) + call lipid_angle(elipang) + endif + else + call lipid_bond(elipbond) + call lipid_angle(elipang) + endif + call lipid_LJ(eliplj) + call lipid_elec(elipelec) + if (nres_molec(1).gt.0) then + call elip_prot(elipidprot) + else + elipidprot=0.0d0 + endif + else + elipbond=0.0d0 + elipang=0.0d0 + eliplj=0.0d0 + elipelec=0.0d0 + endif ! call ecatcat(ecationcation) ! print *,"after ebend", wtor_nucl #ifdef TIMING @@ -976,6 +1092,17 @@ ! energia(50)=ecations_prot_amber energia(50)=ecation_nucl energia(51)=ehomology_constr +! energia(51)=homology + energia(52)=elipbond + energia(53)=elipang + energia(54)=eliplj + energia(55)=elipelec + energia(56)=ecat_prottran + energia(57)=ecation_protang + energia(58)=elipidprot +! write(iout,*) elipelec,"elipelec" +! write(iout,*) elipang,"elipang" +! write(iout,*) eliplj,"eliplj" call sum_energy(energia,.true.) if (dyn_ss) call dyn_set_nss ! print *," Processor",myrank," left SUM_ENERGY" @@ -988,7 +1115,7 @@ end subroutine etotal !----------------------------------------------------------------------------- subroutine sum_energy(energia,reduce) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifndef ISNAN external proc_proc @@ -1019,9 +1146,10 @@ ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,& ecorr3_nucl,ehomology_constr real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,& - ecation_nucl + ecation_nucl,ecat_prottran,ecation_protang real(kind=8) :: escbase,epepbase,escpho,epeppho integer :: i + real(kind=8) :: elipbond,elipang,eliplj,elipelec,elipidprot #ifdef MPI integer :: ierr real(kind=8) :: time00 @@ -1105,6 +1233,13 @@ epeppho=energia(49) ecation_nucl=energia(50) ehomology_constr=energia(51) + elipbond=energia(52) + elipang=energia(53) + eliplj=energia(54) + elipelec=energia(55) + ecat_prottran=energia(56) + ecation_protang=energia(57) + elipidprot=energia(58) ! ecations_prot_amber=energia(50) ! energia(41)=ecation_prot @@ -1118,13 +1253,21 @@ +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+wtube*etube& - +Eafmforce+ethetacnstr+ehomology_constr & + +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+wcatnucl*ecation_nucl + +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl& + +(elipbond+elipang+eliplj+elipelec)*wmartini& + +wcat_tran*ecat_prottran+ecation_protang& + +wlip_prot*elipidprot& +#ifdef WHAM_RUN + +0.0d0 +#else + +ehomology_constr +#endif #else etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) & +wang*ebe+wtor*etors+wscloc*escloc & @@ -1132,13 +1275,21 @@ +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+wtube*etube& - +Eafmforce+ethetacnstr+ehomology_constr & + +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+wcatnucl*ecation_nucl + +wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl& + +(elipbond+elipang+eliplj+elipelec)*wmartini& + +wcat_tran*ecat_prottran+ecation_protang& + +wlip_prot*elipidprot& +#ifdef WHAM_RUN + +0.0d0 +#else + +ehomology_constr +#endif #endif energia(0)=etot ! detecting NaNQ @@ -1166,7 +1317,7 @@ end subroutine sum_energy !----------------------------------------------------------------------------- subroutine rescale_weights(t_bath) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) #ifdef MPI include 'mpif.h' #endif @@ -1256,7 +1407,7 @@ end subroutine rescale_weights !----------------------------------------------------------------------------- subroutine enerprint(energia) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.FFIELD' @@ -1272,9 +1423,9 @@ ebe_nucl,esbloc,etors_nucl,etors_d_nucl,ecorr_nucl,& ecorr3_nucl,ehomology_constr real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,& - ecation_nucl + ecation_nucl,ecat_prottran,ecation_protang real(kind=8) :: escbase,epepbase,escpho,epeppho - + real(kind=8) :: elipbond,elipang,eliplj,elipelec,elipidprot etot=energia(0) evdw=energia(1) evdw2=energia(2) @@ -1327,8 +1478,14 @@ escpho=energia(48) epeppho=energia(49) ecation_nucl=energia(50) + elipbond=energia(52) + elipang=energia(53) + eliplj=energia(54) + elipelec=energia(55) + ecat_prottran=energia(56) + ecation_protang=energia(57) ehomology_constr=energia(51) - + elipidprot=energia(58) ! ecations_prot_amber=energia(50) #ifdef SPLITELE write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,& @@ -1343,9 +1500,12 @@ 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, & + ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,& + ecat_prottran,wcat_tran,ecation_protang,wcat_ang,& + ecationcation,wcatcat, & escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,& - ecation_nucl,wcatnucl,ehomology_constr,etot + ecation_nucl,wcatnucl,ehomology_constr,& + elipbond,elipang,eliplj,elipelec,elipidprot,wlip_prot,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ & @@ -1387,6 +1547,8 @@ '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)'/ & + 'ECATPTRAN=',1pE16.6,' WEIGHT=',1pD16.6,'(cation prot tran)'/ & + 'ECATPANG=',1pE16.6,' WEIGHT=',1pD16.6,'(cation prot angle)'/ & '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)'/ & @@ -1394,6 +1556,11 @@ 'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/& 'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/& 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/& + 'ELIPBOND=',1pE16.6,'(matrini bond energy)'/& + 'ELIPANG=',1pE16.6,'(matrini angle energy)'/& + 'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/& + 'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/& + 'ELIPPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(lipid prot)'/ & 'ETOT= ',1pE16.6,' (total)') #else write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,& @@ -1410,7 +1577,7 @@ 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,& - ecation_nucl,wcatnucl,ehomology_constr,etot + ecation_nucl,wcatnucl,ehomology_constr,elipidprot,wlip_prot,etot 10 format (/'Virtual-chain energies:'// & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ & @@ -1458,6 +1625,11 @@ 'EPEPPHO=',1pE16.6,' WEIGHT=',1pD16.6,'(pep-prot nucl-phosphate)'/& 'ECATBASE=',1pE16.6,' WEIGHT=',1pD16.6,'(cation nucl-base)'/& 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/& + 'ELIPBOND=',1pE16.6,'(matrini bond energy)'/& + 'ELIPANG=',1pE16.6,'(matrini angle energy)'/& + 'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/& + 'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/& + 'ELIPPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(lipid prot)'/ & 'ETOT= ',1pE16.6,' (total)') #endif return @@ -1468,7 +1640,7 @@ ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJ potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' real(kind=8),parameter :: accur=1.0d-10 ! include 'COMMON.GEO' @@ -1649,7 +1821,7 @@ ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJK potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -1753,7 +1925,7 @@ ! use comm_srutu use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -1895,7 +2067,7 @@ ! assuming the Gay-Berne potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -1910,7 +2082,7 @@ ! include 'COMMON.SBRIDGE' logical :: lprn !el local variables - integer :: iint,itypi,itypi1,itypj,subchap,icont + integer :: iint,itypi,itypi1,itypj,subchap,icont,countss 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,& @@ -1923,6 +2095,7 @@ ! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 lprn=.false. + countss=0 ! if (icall.eq.0) lprn=.false. !el ind=0 dCAVdOM2=0.0d0 @@ -1962,7 +2135,8 @@ ! 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) + countss=countss+1 + call dyn_ssbond_ene(i,j,evdwij,countss) evdw=evdw+evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' @@ -2094,7 +2268,7 @@ endif if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2e10.2,e11.3)')& - 'evdw',i,j,evdwij,xi,xj,rij !,"egb" + 'evdw',i,j,evdwij,1.0D0/rij,1.0D0/rij_shift,dabs(aa/bb)**(1.0D0/6.0D0)!,"egb" !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 @@ -2144,7 +2318,7 @@ ! use comm_srutu use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -2291,7 +2465,7 @@ ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJ potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' real(kind=8),parameter :: accur=1.0d-10 ! include 'COMMON.GEO' @@ -2374,7 +2548,7 @@ ! ! Soft-sphere potential of p-p interaction ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CONTROL' ! include 'COMMON.IOUNITS' @@ -2474,7 +2648,7 @@ end subroutine eelec_soft_sphere !----------------------------------------------------------------------------- subroutine vec_and_deriv -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifdef MPI include 'mpif.h' @@ -2661,7 +2835,7 @@ end subroutine vec_and_deriv !----------------------------------------------------------------------------- subroutine check_vecgrad -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.GEO' @@ -2749,7 +2923,7 @@ end subroutine check_vecgrad !----------------------------------------------------------------------------- subroutine set_matrices -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifdef MPI include "mpif.h" @@ -2769,7 +2943,7 @@ ! include 'COMMON.VECTORS' ! include 'COMMON.FFIELD' real(kind=8) :: auxvec(2),auxmat(2,2) - integer :: i,iti1,iti,k,l + integer :: i,iti1,iti,k,l,ii,innt,inct real(kind=8) :: sin1,cos1,sin2,cos2,dwacos2,dwasin2,cost1,sint1,& sint1sq,sint1cub,sint1cost1,b1k,b2k,aux ! print *,"in set matrices" @@ -2784,6 +2958,35 @@ #else do i=3,nres+1 #endif +#ifdef FIVEDIAG + ii=ireschain(i-2) +!c write (iout,*) "i",i,i-2," ii",ii + if (ii.eq.0) cycle + innt=chain_border(1,ii) + inct=chain_border(2,ii) +!c write (iout,*) "i",i,i-2," ii",ii," innt",innt," inct",inct +!c if (i.gt. nnt+2 .and. i.lt.nct+2) then + if (i.gt. innt+2 .and. i.lt.inct+2) then + if (itype(i-2,1).eq.0) then + iti = nloctyp + else + iti = itype2loc(itype(i-2,1)) + endif + else + iti=nloctyp + endif +!c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then + if (i.gt. innt+1 .and. i.lt.inct+1) then +! iti1 = itype2loc(itype(i-1)) + if (itype(i-1,1).eq.0) then + iti1 = nloctyp + else + iti1 = itype2loc(itype(i-1,1)) + endif + else + iti1=nloctyp + endif +#else if (i.gt. nnt+2 .and. i.lt.nct+2) then if (itype(i-2,1).eq.0) then iti = nloctyp @@ -2799,6 +3002,7 @@ else iti1=nloctyp endif +#endif ! print *,i,itype(i-2,1),iti #ifdef NEWCORR cost1=dcos(theta(i-1)) @@ -2886,7 +3090,7 @@ write (iout,*) 'theta=', theta(i-1) #endif #else - if (i.gt. nnt+2 .and. i.lt.nct+2) then + if (i.gt. innt+2 .and. i.lt.inct+2) then ! write(iout,*) "i,",molnum(i),nloctyp ! print *, "i,",molnum(i),i,itype(i-2,1) if (molnum(i).eq.1) then @@ -2943,7 +3147,8 @@ #endif ! print *,i,"i" - if (i .lt. nres+1) then + if (i .lt. nres+1 .and. (itype(i-1,1).lt.ntyp1).and.(itype(i-1,1).ne.0)) then +! if (i .lt. nres+1) then sin1=dsin(phi(i)) cos1=dcos(phi(i)) sintab(i-2)=sin1 @@ -2980,7 +3185,7 @@ Ug2(2,1,i-2)=0.0d0 Ug2(2,2,i-2)=0.0d0 endif - if (i .gt. 3 .and. i .lt. nres+1) then + if (i .gt. 3) then ! .and. i .lt. nres+1) then obrot_der(1,i-2)=-sin1 obrot_der(2,i-2)= cos1 Ugder(1,1,i-2)= sin1 @@ -3393,7 +3598,7 @@ ! the orientation of the CA-CA virtual bonds. ! use comm_locel -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) #ifdef MPI include 'mpif.h' #endif @@ -3625,7 +3830,7 @@ subroutine eelecij(i,j,ees,evdw1,eel_loc) use comm_locel -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifdef MPI include "mpif.h" @@ -4686,7 +4891,7 @@ ! Third- and fourth-order contributions from turns use comm_locel -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.GEO' @@ -4903,7 +5108,7 @@ ! Third- and fourth-order contributions from turns use comm_locel -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.GEO' @@ -5285,7 +5490,7 @@ ! peptide-group centers and side chains and its gradient in virtual-bond and ! side-chain vectors. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -5392,7 +5597,7 @@ ! peptide-group centers and side chains and its gradient in virtual-bond and ! side-chain vectors. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -5405,7 +5610,7 @@ ! include 'COMMON.CONTROL' real(kind=8),dimension(3) :: ggg !el local variables - integer :: i,iint,j,k,iteli,itypj,subchap,icont + integer :: i,iint,j,k,iteli,itypj,subchap,iconta real(kind=8) :: evdw2,evdw2_14,xi,yi,zi,xj,yj,zj,rrij,fac,& e1,e2,evdwij,rij real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& @@ -5418,16 +5623,17 @@ !d write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e ! do i=iatscp_s,iatscp_e if (nres_molec(1).eq.0) return - do icont=g_listscp_start,g_listscp_end - i=newcontlistscpi(icont) - j=newcontlistscpj(icont) + do iconta=g_listscp_start,g_listscp_end +! print *,"icont",iconta,g_listscp_start,g_listscp_end + i=newcontlistscpi(iconta) + j=newcontlistscpj(iconta) 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)) zi=0.5D0*(c(3,i)+c(3,i+1)) call to_box(xi,yi,zi) - +! print *,itel(i),i,j ! do iint=1,nscp_gr(i) ! do j=iscpstart(i,iint),iscpend(i,iint) @@ -5537,7 +5743,7 @@ ! ! Evaluate bridge-strain energy and its gradient in virtual-bond and SC vectors. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.SBRIDGE' ! include 'COMMON.CHAIN' @@ -5545,18 +5751,19 @@ ! include 'COMMON.VAR' ! include 'COMMON.INTERACT' ! include 'COMMON.IOUNITS' - real(kind=8),dimension(3) :: ggg + real(kind=8),dimension(3) :: ggg,vec !el local variables - integer :: i,j,ii,jj,iii,jjj,k - real(kind=8) :: fac,eij,rdis,ehpb,dd,waga + integer :: i,j,ii,jj,iii,jjj,k,mnumii,mnumjj + real(kind=8) :: fac,eij,rdis,ehpb,dd,waga,xi,yi,zi,zj,yj,xj ehpb=0.0D0 -!d write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr -!d write(iout,*)'link_start=',link_start,' link_end=',link_end +! write(iout,*)'edis: nhpb=',nhpb!,' fbr=',fbr +! write(iout,*)'link_start=',link_start,' link_end=',link_end if (link_end.eq.0) return do i=link_start,link_end ! If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a ! CA-CA distance used in regularization of structure. + ii=ihpb(i) jj=jhpb(i) ! iii and jjj point to the residues for which the distance is assigned. @@ -5567,6 +5774,14 @@ iii=ii jjj=jj endif + do j=1,3 + vec(j)=c(j,jj)-c(j,ii) + enddo + mnumii=molnum(iii) + mnumjj=molnum(jjj) + if (energy_dec) write(iout,*) i,ii,jj,mnumii,mnumjj,itype(jjj,mnumjj),itype(iii,mnumii) + if ((itype(iii,mnumii).gt.ntyp_molec(mnumii)).or.(itype(jjj,mnumjj).gt.ntyp_molec(mnumjj))) cycle + ! write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj, ! & dhpb(i),dhpb1(i),forcon(i) ! 24/11/03 AL: SS bridges handled separately because of introducing a specific @@ -5624,6 +5839,7 @@ enddo else dd=dist(ii,jj) + if (constr_dist.eq.11) then ehpb=ehpb+fordepth(i)**4.0d0 & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i)) @@ -5638,11 +5854,29 @@ !c write (iout,*) "alph nmr", !c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i)) else + xi=c(1,ii) + yi=c(2,ii) + zi=c(3,ii) + call to_box(xi,yi,zi) + xj=c(1,jj) + yj=c(2,jj) + zj=c(3,jj) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + vec(1)=xj + vec(2)=yj + vec(3)=zj + dd=sqrt(xj*xj+yj*yj+zj*zj) 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 + if (energy_dec) write (iout,'(a6,2i5,5f10.3)') "edis",ii,jj, & + ehpb,dd,dhpb(i),waga,rdis + !c write (iout,*) "alpha reg",dd,waga*rdis*rdis !C !C Evaluate gradient. @@ -5652,7 +5886,7 @@ endif do j=1,3 - ggg(j)=fac*(c(j,jj)-c(j,ii)) + ggg(j)=fac*vec(j) 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 @@ -5687,7 +5921,7 @@ ! ! A. Liwo and U. Kozlowska, 11/24/03 ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.SBRIDGE' ! include 'COMMON.CHAIN' @@ -5784,7 +6018,7 @@ ! ! Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' ! include 'COMMON.GEO' @@ -5809,6 +6043,10 @@ ! if (.not.allocated(gradbx)) allocate(gradbx(3,nres)) !(3,maxres) do i=ibondp_start,ibondp_end +#ifdef FIVEDIAG + if (itype(i-1,1).eq.ntyp1 .or. itype(i,1).eq.ntyp1) cycle + diff = vbld(i)-vbldp0 +#else 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) @@ -5822,6 +6060,7 @@ else diff = vbld(i)-vbldp0 endif +#endif if (energy_dec) write (iout,'(a7,i5,4f7.3)') & "estr bb",i,vbld(i),vbldp0,diff,AKP*diff*diff estr=estr+diff*diff @@ -5897,7 +6136,7 @@ ! angles gamma and its derivatives in consecutive thetas and gammas. ! use comm_calcthet -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' ! include 'COMMON.GEO' @@ -6038,7 +6277,7 @@ subroutine theteng(thetai,thet_pred_mean,theta0i,ethetai,E_theta,E_tc) use comm_calcthet -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' ! include 'COMMON.IOUNITS' @@ -6133,7 +6372,7 @@ ! ab initio-derived potentials from ! Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203 ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' ! include 'COMMON.GEO' @@ -6344,7 +6583,7 @@ ! ALPHA and OMEGA. ! use comm_sccalc -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.LOCAL' @@ -6469,7 +6708,7 @@ subroutine enesc(x,escloci,dersc,ddersc,mixed) use comm_sccalc -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.LOCAL' @@ -6578,7 +6817,7 @@ subroutine enesc_bound(x,escloci,dersc,dersc12,mixed) use comm_sccalc -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.LOCAL' @@ -6659,7 +6898,7 @@ ! added by Urszula Kozlowska. 07/11/2007 ! use comm_sccalc -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.LOCAL' @@ -6677,11 +6916,11 @@ real(kind=8),dimension(65) :: 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 - real(kind=8) :: s1_t,s1_6_t,s2_t,s2_6_t + real(kind=8) :: s1_t,s1_6_t,s2_t,s2_6_t,gradene 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 !el local variables - integer :: i,j,k !el,it,nlobit + integer :: i,j,k,iti !el,it,nlobit real(kind=8) :: cosfac2,sinfac2,cosfac,sinfac,escloc,delta !el real(kind=8) :: time11,time12,time112,theti !el common /sccalc/ time11,time12,time112,theti,it,nlobit @@ -6700,6 +6939,9 @@ delta=0.02d0*pi escloc=0.0D0 do i=loc_start,loc_end + gscloc(:,i)=0.0d0 + gsclocx(:,i)=0.0d0 +! th_gsclocm1(:,i-1)=0.0d0 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)) @@ -6710,7 +6952,50 @@ sinfac2=0.5d0/(1.0d0-costtab(i+1)) sinfac=dsqrt(sinfac2) it=iabs(itype(i,1)) + iti=it + if (iti.eq.ntyp1 .or. iti.eq.10) cycle +!c AL 3/30/2022 handle the cases of an isolated-residue chain + if (i.eq.nnt .and. itype(i+1,1).eq.ntyp1) cycle + if (i.eq.nct .and. itype(i-1,1).eq.ntyp1) cycle +! costtab(i+1) =dcos(theta(i+1)) if (it.eq.10) goto 1 +#ifdef SC_END + if (i.eq.nct .or. itype(i+1,1).eq.ntyp1) then +!c AL 3/30/2022 handle a sidechain of a loose C-end + cossc1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres)) + sumene=arotam_end(0,1,iti)+& + tschebyshev(1,nterm_scend(1,iti),arotam_end(1,1,iti),cossc1) + escloc=escloc+sumene + gradene=gradtschebyshev(0,nterm_scend(1,iti)-1,& + arotam_end(1,1,iti),cossc1) + gscloc(:,i-1)=gscloc(:,i-1)+& + vbld_inv(i)*(dC_norm(:,i+nres)-dC_norm(:,i-1)& + *cossc1)*gradene + gsclocx(:,i)=gsclocx(:,i)+vbld_inv(i+nres)*& + (dC_norm(:,i-1)-dC_norm(:,i+nres)*cossc1)*gradene +#ifdef ENERGY_DEC + if (energy_dec) write (2,'(2hC ,a3,i6,2(a,f10.5))')& + restyp(iti,1),i," angle",rad2deg*dacos(cossc1)," escloc",sumene +#endif + else if (i.eq.nnt .or. itype(i-1,1).eq.ntyp1) then +!c AL 3/30/2022 handle a sidechain of a loose N-end + cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres)) + sumene=arotam_end(0,2,iti)+& + tschebyshev(1,nterm_scend(2,iti),arotam_end(1,2,iti),cossc) + escloc=escloc+sumene + gradene=gradtschebyshev(0,nterm_scend(2,iti)-1,& + arotam_end(1,2,iti),cossc) + gscloc(:,i)=gscloc(:,i)+& + vbld_inv(i+1)*(dC_norm(:,i+nres)-dC_norm(:,i)& + *cossc)*gradene + gsclocx(:,i)=gsclocx(:,i)+vbld_inv(i+nres)*& + (dC_norm(:,i)-dC_norm(:,i+nres)*cossc)*gradene +#ifdef ENERGY_DEC + if (energy_dec) write (2,'(2hN ,a3,i6,2(a,f10.5))') + & restyp(iti),i," angle",rad2deg*dacos(cossc)," escloc",sumene +#endif + else +#endif ! ! Compute the axes of tghe local cartesian coordinates system; store in ! x_prime, y_prime and z_prime @@ -6989,7 +7274,9 @@ ! & (gscloc(k,i),k=1,3),(gsclocx(k,i),k=1,3) ! to check gradient call subroutine check_grad - +#ifdef SC_END + endif +#endif 1 continue enddo return @@ -7070,7 +7357,7 @@ end subroutine gcont !----------------------------------------------------------------------------- subroutine splinthet(theti,delta,ss,ssder) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -7119,7 +7406,7 @@ #ifdef CRYST_TOR !----------------------------------------------------------------------------- subroutine etor(etors,edihcnstr) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -7221,7 +7508,7 @@ return end subroutine etor_d !----------------------------------------------------------------------------- -c LICZENIE WIEZOW Z ROWNANIA ENERGII MODELLERA +!c LICZENIE WIEZOW Z ROWNANIA ENERGII MODELLERA subroutine e_modeller(ehomology_constr) real(kind=8) :: ehomology_constr ehomology_constr=0.0d0 @@ -7232,7 +7519,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! #else !----------------------------------------------------------------------------- subroutine etor(etors) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -7325,7 +7612,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! gradvalst2,etori logical lprn integer :: i,j,itori,itori1,nval,k,l - +! lprn=.true. if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode etors=0.0D0 do i=iphi_start,iphi_end @@ -7488,7 +7775,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine etor_d(etors_d) ! 6/23/01 Compute double torsional energy -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -8296,7 +8583,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! residues) and the torsional potentials dependent on all 20 types ! of residues computed from AM1 energy surfaces of terminally-blocked ! amino-acid residues. -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -8377,7 +8664,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! the idea of Skolnick et al. If side chains I and J make a contact and ! at the same time side chains I+1 and J+1 make a contact, an extra ! contribution equal to sqrt(eps(i,j)*eps(i+1,j+1)) is added. -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.DERIV' @@ -8435,7 +8722,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine multibody !----------------------------------------------------------------------------- real(kind=8) function esccorr(i,j,k,l,jj,kk) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.DERIV' @@ -8477,7 +8764,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) ! This subroutine calculates multi-body contributions to hydrogen-bonding -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' #ifdef MPI @@ -8790,7 +9077,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine multibody_hb !----------------------------------------------------------------------------- subroutine add_hb_contact(ii,jj,itask) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include "DIMENSIONS" ! include "COMMON.IOUNITS" ! include "COMMON.CONTACTS" @@ -8847,7 +9134,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1) ! This subroutine calculates multi-body contributions to hydrogen-bonding -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' integer,parameter :: max_dim=70 @@ -9241,7 +9528,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine multibody_eello !----------------------------------------------------------------------------- subroutine add_hb_contact_eello(ii,jj,itask) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include "DIMENSIONS" ! include "COMMON.IOUNITS" ! include "COMMON.CONTACTS" @@ -9296,7 +9583,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine add_hb_contact_eello !----------------------------------------------------------------------------- real(kind=8) function ehbcorr(i,j,k,l,jj,kk,coeffp,coeffm) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.DERIV' @@ -9463,7 +9750,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! #ifdef MOMENT !----------------------------------------------------------------------------- subroutine dipole(i,j,jj) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -9536,7 +9823,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! the fourth-, fifth-, and sixth-order local-electrostatic terms. ! use comm_kut -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -9917,7 +10204,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine kernel !----------------------------------------------------------------------------- real(kind=8) function eello4(i,j,k,l,jj,kk) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10032,7 +10319,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end function eello4 !----------------------------------------------------------------------------- real(kind=8) function eello5(i,j,k,l,jj,kk) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10440,7 +10727,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end function eello5 !----------------------------------------------------------------------------- real(kind=8) function eello6(i,j,k,l,jj,kk) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10585,7 +10872,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- real(kind=8) function eello6_graph1(i,j,k,l,imat,swap) use comm_kut -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10693,7 +10980,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- real(kind=8) function eello6_graph2(i,j,k,l,jj,kk,swap) use comm_kut -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10880,7 +11167,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end function eello6_graph2 !----------------------------------------------------------------------------- real(kind=8) function eello6_graph3(i,j,k,l,jj,kk,swap) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -10998,7 +11285,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end function eello6_graph3 !----------------------------------------------------------------------------- real(kind=8) function eello6_graph4(i,j,k,l,jj,kk,imat,swap) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -11245,7 +11532,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end function eello6_graph4 !----------------------------------------------------------------------------- real(kind=8) function eello_turn6(i,jj,kk) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -11581,7 +11868,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! #ifndef OSF !DEC$ ATTRIBUTES FORCEINLINE::MATVEC2 #endif -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' real(kind=8),dimension(2) :: V1,V2 real(kind=8),dimension(2,2) :: A1 @@ -11604,7 +11891,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! #ifndef OSF !DEC$ ATTRIBUTES FORCEINLINE::MATMAT2 #endif -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' real(kind=8),dimension(2,2) :: A1,A2,A3 real(kind=8) :: ai3_11,ai3_12,ai3_21,ai3_22 @@ -11716,7 +12003,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! energy_p_new_barrier.F !----------------------------------------------------------------------------- subroutine sum_gradient -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) use io_base, only: pdbout ! include 'DIMENSIONS' #ifndef ISNAN @@ -11836,7 +12123,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! wscbase*gvdwc_scbase(j,i)+ & wpepbase*gvdwc_pepbase(j,i)+& wscpho*gvdwc_scpho(j,i)+ & - wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i) + wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)+ & + wmartini*(gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i))+& + wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)+& + wlip_prot*gradpepmart(j,i) + @@ -11874,7 +12165,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! wscbase*gvdwc_scbase(j,i)+ & wpepbase*gvdwc_pepbase(j,i)+& wscpho*gvdwc_scpho(j,i)+& - wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i) + wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)+& + wmartini*(gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i))+& + wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)+& + wlip_prot*gradpepmart(j,i) + enddo @@ -12035,7 +12330,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! +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) + +wbond_nucl*gradb_nucl(j,i)+wsbloc*gsbloc(j,i)!& +! + gradcattranc(j,i) ! if (i.eq.21) then ! print *,"in sum",gradc(j,i,icg),wturn4*gcorr4_turn(j,i),& ! wturn4*gshieldc_t4(j,i), & @@ -12115,7 +12411,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! +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)+wcatnucl*gradnuclcat(j,i) + +wsbloc*gsbloc(j,i)+wcatnucl*gradnuclcat(j,i)!& +! + gradcattranc(j,i) @@ -12142,7 +12439,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! +wcatprot* gradpepcatx(j,i)& +wscbase*gvdwx_scbase(j,i) & +wpepbase*gvdwx_pepbase(j,i)& - +wscpho*gvdwx_scpho(j,i)+wcatnucl*gradnuclcatx(j,i) + +wscpho*gvdwx_scpho(j,i)+wcatnucl*gradnuclcatx(j,i)& + +wcat_tran*gradcattranx(j,i)+gradcatangx(j,i)& + +wlip_prot*gradpepmartx(j,i) + ! if (i.eq.3) print *,"tu?", wscpho,gvdwx_scpho(j,i) enddo @@ -12357,7 +12657,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! end subroutine sum_gradient !----------------------------------------------------------------------------- subroutine sc_grad -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) use calc_data ! include 'DIMENSIONS' ! include 'COMMON.CHAIN' @@ -12453,9 +12753,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut ! write (iout,*) "gg",(gg(k),k=1,3) do k=1,3 - gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k) & + gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k)*sss_ele_cut & +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) & - +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv + +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut ! gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) & ! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) & @@ -12470,8 +12770,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! Calculate the components of the gradient in DC and X ! do l=1,3 - gradpepcat(l,i)=gradpepcat(l,i)-gg(l) - gradpepcat(l,j)=gradpepcat(l,j)+gg(l) + gradpepcat(l,i)=gradpepcat(l,i)-gg(l)*sss_ele_cut + gradpepcat(l,j)=gradpepcat(l,j)+gg(l)*sss_ele_cut enddo end subroutine sc_grad_cat @@ -12491,20 +12791,21 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! eom2=0.0d0 ! eom12=evdwij*eps1_om12 ! end diagnostics +! write (iout,*) "gg",(gg(k),k=1,3) 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)) & + gradpepcat(k,i)= gradpepcat(k,i) +sss_ele_cut*(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)) & + - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0) + gradpepcat(k,i+1)= gradpepcat(k,i+1) +sss_ele_cut*(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 - gradpepcat(k,j)=gradpepcat(k,j)+gg(k) + + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0) + gradpepcat(k,j)=gradpepcat(k,j)+gg(k)*sss_ele_cut enddo end subroutine sc_grad_cat_pep @@ -12513,7 +12814,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! subroutine mixder(thetai,thet_pred_mean,theta0i,E_tc_t) use comm_calcthet -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.LOCAL' ! include 'COMMON.IOUNITS' @@ -12590,7 +12891,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! Version of March '95, based on an early version of November '91. ! !********************************************************************** -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.CHAIN' @@ -12609,7 +12910,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! sint2,xp,yp,xxp,yyp,zzp,dj ! common /przechowalnia/ fromto +#ifdef FIVEDIAG + if(.not. allocated(fromto)) allocate(fromto(3,3)) +#else if(.not. allocated(fromto)) allocate(fromto(3,3,maxdim)) +#endif ! get the position of the jth ijth fragment of the chain coordinate system ! in the fromto array. ! indmat(i,j)=((2*(nres-2)-i)*(i-1))/2+j-1 @@ -12648,6 +12953,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! ! generate the matrix products of type r(i)t(i)...r(j)t(j) ! +#ifndef FIVEDIAG do i=2,nres-2 ind=indmat(i,i+1) do k=1,3 @@ -12660,6 +12966,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! fromto(k,l,ind)=temp(k,l) enddo enddo + do j=i+1,nres-2 ind=indmat(i,j+1) do k=1,3 @@ -12679,6 +12986,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! enddo enddo enddo +#endif ! ! Calculate derivatives. ! @@ -12776,6 +13084,19 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ind1=ind1+1 ind=indmat(i+1,j+1) !d print *,'i=',i,' j=',j,' ind=',ind,' ind1=',ind1 +#ifdef FIVEDIAG + call build_fromto(i+1,j+1,fromto) +!c write(iout,'(7hfromto 9f10.5)')((fromto(k,l),l=1,3),k=1,3) + do k=1,3 + do l=1,3 + tempkl=0.0D0 + do m=1,2 + tempkl=tempkl+prordt(k,m,i)*fromto(m,l) + enddo + temp(k,l)=tempkl + enddo + enddo +#else do k=1,3 do l=1,3 tempkl=0.0D0 @@ -12785,6 +13106,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! temp(k,l)=tempkl enddo enddo +#endif !d print '(9f8.3)',((fromto(k,l,ind),l=1,3),k=1,3) !d print '(9f8.3)',((prod(k,l,i),l=1,3),k=1,3) !d print '(9f8.3)',((temp(k,l),l=1,3),k=1,3) @@ -12804,6 +13126,17 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! !--- Calculate the derivatives in phi ! +#ifdef FIVEDIAG + do k=1,3 + do l=1,3 + tempkl=0.0D0 + do m=1,3 + tempkl=tempkl+prodrt(k,m,i)*fromto(m,l) + enddo + temp(k,l)=tempkl + enddo + enddo +#else do k=1,3 do l=1,3 tempkl=0.0D0 @@ -12813,6 +13146,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! temp(k,l)=tempkl enddo enddo +#endif + + do k=1,3 dcdv(k+3,ind1)=vbld(i+1)*temp(k,1) enddo @@ -12877,12 +13213,64 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! enddo return end subroutine cartder +#ifdef FIVEDIAG + subroutine build_fromto(i,j,fromto) + implicit none + integer i,j,jj,k,l,m + double precision fromto(3,3),temp(3,3),dp(3,3) + double precision dpkl + save temp +! +! generate the matrix products of type r(i)t(i)...r(j)t(j) on the fly +! +! write (iout,*) "temp on entry" +! write (iout,'(3f10.5)') ((temp(k,l),l=1,3),k=1,3) +! do i=2,nres-2 +! ind=indmat(i,i+1) + if (j.eq.i+1) then + do k=1,3 + do l=1,3 + temp(k,l)=rt(k,l,i) + enddo + enddo + do k=1,3 + do l=1,3 + fromto(k,l)=temp(k,l) + enddo + enddo + else +! do j=i+1,nres-2 +! ind=indmat(i,j+1) + do k=1,3 + do l=1,3 + dpkl=0.0d0 + do m=1,3 + dpkl=dpkl+temp(k,m)*rt(m,l,j-1) + enddo + dp(k,l)=dpkl + fromto(k,l)=dpkl + enddo + enddo + do k=1,3 + do l=1,3 + temp(k,l)=dp(k,l) + enddo + enddo + endif +! write (iout,*) "temp upon exit" +! write (iout,'(3f10.5)') ((temp(k,l),l=1,3),k=1,3) +! enddo +! enddo + return + end subroutine build_fromto +#endif + !----------------------------------------------------------------------------- ! checkder_p.F !----------------------------------------------------------------------------- subroutine check_cartgrad ! Check the gradient of Cartesian coordinates in internal coordinates. -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.VAR' @@ -13058,7 +13446,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine check_ecart ! Check the gradient of the energy in Cartesian coordinates. -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CHAIN' ! include 'COMMON.DERIV' @@ -13066,8 +13454,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! include 'COMMON.VAR' ! include 'COMMON.CONTACTS' use comm_srutu +!#ifdef LBFGS +! use minimm, only: funcgrad +!#endif !el integer :: icall !el common /srutu/ icall +! real(kind=8) :: funcgrad real(kind=8),dimension(6) :: ggg real(kind=8),dimension(3) :: cc,xx,ddc,ddx real(kind=8),dimension(6*nres) :: x,g !(maxvar) (maxvar=6*maxres) @@ -13077,7 +13469,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! real(kind=8) :: urparm(1) !EL external fdum integer :: nf,i,j,k - real(kind=8) :: aincr,etot,etot1 + real(kind=8) :: aincr,etot,etot1,ff icg=1 nf=0 nfl=0 @@ -13089,8 +13481,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call geom_to_var(nvar,x) call etotal(energia) etot=energia(0) +#ifdef LBFGS + ff=funcgrad(x,g) +#else !el call enerprint(energia) call gradient(nvar,x,nf,g,uiparm,urparm,fdum) +#endif icall =1 do i=1,nres write (iout,'(i5,3f10.5)') i,(gradxorr(j,i),j=1,3) @@ -13183,8 +13579,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! call intcartderiv ! call checkintcartgrad call zerograd - aincr=1.0D-5 - write(iout,*) 'Calling CHECK_ECARTINT.' + aincr=graddelta + write(iout,*) 'Calling CHECK_ECARTINT.,kupa' nf=0 icall=0 call geom_to_var(nvar,x) @@ -13195,6 +13591,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call etotal(energia) etot=energia(0) call cartgrad +#ifdef FIVEDIAG + call grad_transform +#endif icall =1 do i=1,nres write (iout,'(i5,3f10.5)') i,(gradxorr(j,i),j=1,3) @@ -13207,19 +13606,23 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! grad_s(j,i)=gcart(j,i) grad_s(j+3,i)=gxcart(j,i) write(iout,*) "before movement analytical gradient" + + enddo + enddo do i=1,nres write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),& (gxcart(j,i),j=1,3) enddo - enddo - enddo else !- split gradient check call zerograd call etotal_long(energia) !el call enerprint(energia) call cartgrad +#ifdef FIVEDIAG + call grad_transform +#endif icall =1 do i=1,nres write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),& @@ -13238,6 +13641,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call etotal_short(energia) call enerprint(energia) call cartgrad +#ifdef FIVEDIAG + call grad_transform +#endif + icall =1 do i=1,nres write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3),& @@ -13254,8 +13661,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! enddo endif write (iout,'(/a/)') 'Gradient in virtual-bond and SC vectors' -! do i=1,nres +#ifdef FIVEDIAG + do i=1,nres +#else do i=nnt,nct +#endif 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) @@ -13277,7 +13687,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call zerograd call etotal(energia1) etot1=energia1(0) - write (iout,*) "ij",i,j," etot1",etot1 +! write (iout,*) "ij",i,j," etot1",etot1 else !- split gradient call etotal_long(energia1) @@ -13298,7 +13708,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call zerograd call etotal(energia1) etot2=energia1(0) - write (iout,*) "ij",i,j," etot2",etot2 +! write (iout,*) "ij",i,j," etot2",etot2 ggg(j)=(etot1-etot2)/(2*aincr) else !- split gradient @@ -13426,7 +13836,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! if (.not.split_ene) then call etotal(energia) etot=energia(0) -!el call enerprint(energia) +! call enerprint(energia) call cartgrad icall =1 do i=1,nres @@ -13529,6 +13939,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! if (.not.split_ene) then call zerograd call etotal(energia1) +! call enerprint(energia1) etot2=energia1(0) ggg(j)=(etot1-etot2)/(2*aincr) else @@ -13560,7 +13971,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! if (.not.split_ene) then call zerograd call etotal(energia1) +! call enerprint(energia1) etot1=energia1(0) +! print *,"ene",energia1(0),energia1(57) else !- split gradient call etotal_long(energia1) @@ -13584,6 +13997,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! call zerograd call etotal(energia1) etot2=energia1(0) +! call enerprint(energia1) +! print *,"ene",energia1(0),energia1(57) ggg(j+3)=(etot1-etot2)/(2*aincr) else !- split gradient @@ -13616,7 +14031,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine check_eint ! Check the gradient of energy in internal coordinates. -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CHAIN' ! include 'COMMON.DERIV' @@ -13624,8 +14039,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! include 'COMMON.VAR' ! include 'COMMON.GEO' use comm_srutu +!#ifdef LBFGS +! use minimm, only : funcgrad +!#endif !el integer :: icall !el common /srutu/ icall +! real(kind=8) :: funcgrad real(kind=8),dimension(6*nres) :: x,gana,gg !(maxvar) (maxvar=6*maxres) integer :: uiparm(1) real(kind=8) :: urparm(1) @@ -13633,7 +14052,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! character(len=6) :: key !EL external fdum integer :: i,ii,nf - real(kind=8) :: xi,aincr,etot,etot1,etot2 + real(kind=8) :: xi,aincr,etot,etot1,etot2,ff call zerograd aincr=1.0D-7 print '(a)','Calling CHECK_INT.' @@ -13659,9 +14078,14 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! #endif nf=1 nfl=3 +#ifdef LBFGS + ff=funcgrad(x,gana) +#else + !d write (iout,'(10f8.3)') (rad2deg*x(i),i=1,nvar) call gradient(nvar,x,nf,gana,uiparm,urparm,fdum) !d write (iout,'(i3,1pe14.4)') (i,gana(i),i=1,nvar+20) !sp +#endif icall=1 do i=1,nvar xi=x(i) @@ -13706,7 +14130,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! !----------------------------------------------------------------------------- subroutine Econstr_back ! MD with umbrella_sampling using Wolyne's distance measure as a constraint -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CONTROL' ! include 'COMMON.VAR' @@ -13832,6 +14256,66 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! endif return end function sscale_grad +!SCALINING MARTINI + real(kind=8) function sscale_martini(r) +! include "COMMON.SPLITELE" + real(kind=8) :: r,gamm +! print *,"here2",r_cut_mart,r + if(r.lt.r_cut_mart-rlamb_mart) then + sscale_martini=1.0d0 + else if(r.le.r_cut_mart.and.r.ge.r_cut_mart-rlamb_mart) then + gamm=(r-(r_cut_mart-rlamb_mart))/rlamb_mart + sscale_martini=1.0d0+gamm*gamm*(2*gamm-3.0d0) + else + sscale_martini=0.0d0 + endif + return + end function sscale_martini + real(kind=8) function sscale_grad_martini(r) +! include "COMMON.SPLITELE" + real(kind=8) :: r,gamm + if(r.lt.r_cut_mart-rlamb_mart) then + sscale_grad_martini=0.0d0 + else if(r.le.r_cut_mart.and.r.ge.r_cut_mart-rlamb_mart) then + gamm=(r-(r_cut_mart-rlamb_mart))/rlamb_mart + sscale_grad_martini=gamm*(6*gamm-6.0d0)/rlamb_mart + else + sscale_grad_martini=0.0d0 + endif + return + end function sscale_grad_martini + real(kind=8) function sscale_martini_angle(r) +! include "COMMON.SPLITELE" + real(kind=8) :: r,gamm,r_cut_angle,rlamb_angle +! print *,"here2",r_cut_angle,r + r_cut_angle=3.12d0 + rlamb_angle=0.1d0 + if(r.lt.r_cut_angle-rlamb_angle) then + sscale_martini_angle=1.0d0 + else if(r.le.r_cut_angle.and.r.ge.r_cut_angle-rlamb_angle) then + gamm=(r-(r_cut_angle-rlamb_angle))/rlamb_angle + sscale_martini_angle=1.0d0+gamm*gamm*(2*gamm-3.0d0) + else + sscale_martini_angle=0.0d0 + endif + return + end function sscale_martini_angle + real(kind=8) function sscale_grad_martini_angle(r) +! include "COMMON.SPLITELE" + real(kind=8) :: r,gamm,r_cut_angle,rlamb_angle + r_cut_angle=3.12d0 + rlamb_angle=0.1d0 + if(r.lt.r_cut_angle-rlamb_angle) then + sscale_grad_martini_angle=0.0d0 + else if(r.le.r_cut_angle.and.r.ge.r_cut_angle-rlamb_angle) then + gamm=(r-(r_cut_angle-rlamb_angle))/rlamb_angle + sscale_grad_martini_angle=gamm*(6*gamm-6.0d0)/rlamb_angle + else + sscale_grad_martini_angle=0.0d0 + endif + return + end function sscale_grad_martini_angle + !!!!!!!!!! PBCSCALE real(kind=8) function sscale_ele(r) @@ -13861,6 +14345,35 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! endif return end function sscagrad_ele +!!!!!!!!!! PBCSCALE + real(kind=8) function sscale2(r,r_cc,r_ll) +! include "COMMON.SPLITELE" + real(kind=8) :: r,gamm,r_cc,r_ll + if(r.lt.r_cc-r_ll) then + sscale2=1.0d0 + else if(r.le.r_cc.and.r.ge.r_cc-r_ll) then + gamm=(r-(r_cc-r_ll))/r_ll + sscale2=1.0d0+gamm*gamm*(2*gamm-3.0d0) + else + sscale2=0d0 + endif + return + end function sscale2 + + real(kind=8) function sscagrad2(r,r_cc,r_ll) + real(kind=8) :: r,gamm,r_cc,r_ll +! include "COMMON.SPLITELE" + if(r.lt.r_cc-r_ll) then + sscagrad2=0.0d0 + else if(r.le.r_cc.and.r.ge.r_cc-r_ll) then + gamm=(r-(r_cc-r_ll))/r_ll + sscagrad2=gamm*(6*gamm-6.0d0)/r_ll + else + sscagrad2=0.0d0 + endif + return + end function sscagrad2 + real(kind=8) function sscalelip(r) real(kind=8) r,gamm sscalelip=1.0d0+r*r*(2.0d0*r-3.0d0) @@ -13880,7 +14393,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJ potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -13982,7 +14495,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJ potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14078,7 +14591,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJK potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14172,7 +14685,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! This subroutine calculates the interaction energy of nonbonded side chains ! assuming the LJK potential of interaction. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14271,7 +14784,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! ! assuming the Berne-Pechukas potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14325,10 +14838,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!! if (itypj.eq.ntyp1) cycle ! dscj_inv=dsc_inv(itypj) dscj_inv=vbld_inv(j+nres) -chi1=chi(itypi,itypj) -chi2=chi(itypj,itypi) -chi12=chi1*chi2 -chip1=chip(itypi) +!chi1=chi(itypi,itypj) +!chi2=chi(itypj,itypi) +!chi12=chi1*chi2 +!chip1=chip(itypi) alf1=alp(itypi) alf2=alp(itypj) alf12=0.5D0*(alf1+alf2) @@ -14401,7 +14914,7 @@ chip1=chip(itypi) ! assuming the Berne-Pechukas potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14534,7 +15047,7 @@ chip1=chip(itypi) ! assuming the Gay-Berne potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14733,7 +15246,7 @@ chip1=chip(itypi) ! assuming the Gay-Berne potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -14747,7 +15260,7 @@ chip1=chip(itypi) ! include 'COMMON.CONTROL' logical :: lprn !el local variables - integer :: iint,itypi,itypi1,itypj,subchap + integer :: iint,itypi,itypi1,itypj,subchap,countss real(kind=8) :: rrij,xi,yi,zi,fac,sigm,epsi,sig0ij,sig real(kind=8) :: sss,e1,e2,evdw,rij_shift,sss_grad real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& @@ -14758,6 +15271,7 @@ chip1=chip(itypi) ! print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon evdw=0.0D0 lprn=.false. + countss=0 ! if (icall.eq.0) lprn=.false. !el ind=0 do i=iatsc_s,iatsc_e @@ -14784,7 +15298,8 @@ chip1=chip(itypi) 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) + countss=countss+1 + call dyn_ssbond_ene(i,j,evdwij,countss) evdw=evdw+evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' @@ -14935,7 +15450,7 @@ chip1=chip(itypi) ! assuming the Gay-Berne-Vorobjev potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -15077,7 +15592,7 @@ chip1=chip(itypi) ! assuming the Gay-Berne-Vorobjev potential of interaction. ! use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -15220,7 +15735,7 @@ chip1=chip(itypi) ! The potential depends both on the distance of peptide-group centers and on ! the orientation of the CA-CA virtual bonds. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) use comm_locel #ifdef MPI @@ -15299,7 +15814,7 @@ chip1=chip(itypi) #endif ! print *, "before set matrices" call set_matrices -! print *,"after set martices" +! print *,"after set catices" #ifdef TIMING time_mat=time_mat+MPI_Wtime()-time01 #endif @@ -15416,7 +15931,7 @@ chip1=chip(itypi) end subroutine eelec_scale !----------------------------------------------------------------------------- subroutine eelecij_scale(i,j,ees,evdw1,eel_loc) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) use comm_locel ! include 'DIMENSIONS' @@ -16191,7 +16706,7 @@ chip1=chip(itypi) ! ! Compute Evdwpp ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CONTROL' ! include 'COMMON.IOUNITS' @@ -16322,7 +16837,7 @@ chip1=chip(itypi) ! peptide-group centers and side chains and its gradient in virtual-bond and ! side-chain vectors. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -16442,7 +16957,7 @@ chip1=chip(itypi) ! peptide-group centers and side chains and its gradient in virtual-bond and ! side-chain vectors. ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -16564,7 +17079,7 @@ chip1=chip(itypi) ! energy_p_new-sep_barrier.F !----------------------------------------------------------------------------- subroutine sc_grad_scale(scalfac) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) use calc_data ! include 'DIMENSIONS' ! include 'COMMON.CHAIN' @@ -16628,7 +17143,7 @@ chip1=chip(itypi) ! ! Compute the long-range slow-varying contributions to the energy ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' use MD_data, only: totT,usampl,eq_time #ifndef ISNAN @@ -16877,7 +17392,7 @@ chip1=chip(itypi) ! ! Compute the short-range fast-varying contributions to the energy ! -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifndef ISNAN external proc_proc @@ -17056,7 +17571,7 @@ chip1=chip(itypi) ! ! Calculate the disulfide-bridge and other energy and the contributions ! from other distance constraints. - call edis(ehpb) +! call edis(ehpb) ! ! Calculate the virtual-bond-angle energy. ! @@ -17249,10 +17764,11 @@ chip1=chip(itypi) !----------------------------------------------------------------------------- ! gradient_p.F !----------------------------------------------------------------------------- +#ifndef LBFGS subroutine gradient(n,x,nf,g,uiparm,urparm,ufparm) use io_base, only:intout,briefout -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CHAIN' ! include 'COMMON.DERIV' @@ -17354,11 +17870,12 @@ chip1=chip(itypi) !d write (iout,'(i3,1pe15.5)') (k,g(k),k=1,n) return end subroutine gradient +#endif !----------------------------------------------------------------------------- subroutine func(n,x,nf,f,uiparm,urparm,ufparm) !from minimize_p.F use comm_chu -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.DERIV' ! include 'COMMON.IOUNITS' @@ -17394,7 +17911,7 @@ chip1=chip(itypi) end subroutine func !----------------------------------------------------------------------------- subroutine cartgrad -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' use energy_data use MD_data, only: totT,usampl,eq_time @@ -17426,13 +17943,13 @@ chip1=chip(itypi) #endif !#define DEBUG !el write (iout,*) "After sum_gradient" -!#ifdef DEBUG -! write (iout,*) "After sum_gradient" -! do i=1,nres-1 -! write (iout,*) i," gradc ",(gradc(j,i,icg),j=1,3) -! write (iout,*) i," gradx ",(gradx(j,i,icg),j=1,3) -! enddo -!#endif +#ifdef DEBUG + write (iout,*) "After sum_gradient" + do i=1,nres-1 + write (iout,*) i," gradc ",(gradc(j,i,icg),j=1,3) + write (iout,*) i," gradx ",(gradx(j,i,icg),j=1,3) + enddo +#endif !#undef DEBUG ! If performing constraint dynamics, add the gradients of the constraint energy if(usampl.and.totT.gt.eq_time) then @@ -17497,27 +18014,28 @@ chip1=chip(itypi) #ifdef DEBUG 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) +! 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 +! 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 +! 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 +! 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 +! call grad_transform #endif #ifdef TIMING time_cartgrad=time_cartgrad+MPI_Wtime()-time00 @@ -17525,9 +18043,66 @@ chip1=chip(itypi) !#undef DEBUG return end subroutine cartgrad + +#ifdef FIVEDIAG + subroutine grad_transform + implicit none +#ifdef MPI + include 'mpif.h' +#endif + integer i,j,kk,mnum +#ifdef DEBUG + write (iout,*)"Converting virtual-bond gradient to CA/SC gradient" + write (iout,*) "dC/dX gradient" + do i=0,nres + write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3), + & (gxcart(j,i),j=1,3) + enddo +#endif + do i=nres,1,-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 + do i=2,nres + mnum=molnum(i) + if (itype(i-1,mnum).eq.ntyp1_molec(mnum) .and.& + itype(i,mnum).ne.ntyp1_molec(mnum)) then + gcart(:,i)=gcart(:,i)+gcart(:,i-1) + else if (itype(i-1,mnum).ne.ntyp1_molec(mnum).and.& + itype(i,mnum).eq.ntyp1_molec(mnum)) then + gcart(:,i-1)=gcart(:,i-1)+gcart(:,i) + endif + enddo +! if (nnt.gt.1) then +! do j=1,3 +! 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 +#ifdef DEBUG + write (iout,*) "CA/SC gradient" + do i=1,nres + write (iout,'(i5,3f10.5,5x,3f10.5)') i,(gcart(j,i),j=1,3), + & (gxcart(j,i),j=1,3) + enddo +#endif + return + end subroutine grad_transform +#endif + !----------------------------------------------------------------------------- subroutine zerograd - ! implicit real*8 (a-h,o-z) + ! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.DERIV' ! include 'COMMON.CHAIN' @@ -17660,6 +18235,16 @@ chip1=chip(itypi) gvdwc_peppho(j,i)=0.0d0 gradnuclcatx(j,i)=0.0d0 gradnuclcat(j,i)=0.0d0 + gradlipbond(j,i)=0.0d0 + gradlipang(j,i)=0.0d0 + gradliplj(j,i)=0.0d0 + gradlipelec(j,i)=0.0d0 + gradcattranc(j,i)=0.0d0 + gradcattranx(j,i)=0.0d0 + gradcatangx(j,i)=0.0d0 + gradcatangc(j,i)=0.0d0 + gradpepmart(j,i)=0.0d0 + gradpepmartx(j,i)=0.0d0 duscdiff(j,i)=0.0d0 duscdiffx(j,i)=0.0d0 enddo @@ -17726,7 +18311,7 @@ chip1=chip(itypi) ! intcartderiv.F !----------------------------------------------------------------------------- subroutine intcartderiv - ! implicit real*8 (a-h,o-z) + ! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifdef MPI include 'mpif.h' @@ -17817,7 +18402,7 @@ chip1=chip(itypi) #else do i=3,nres #endif - if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1).and.molnum(i).ne.5) then + if ((itype(i-1,1).ne.10).and.(itype(i-1,1).ne.ntyp1).and.molnum(i).lt.4) then cost1=dcos(omicron(1,i)) sint1=sqrt(1-cost1*cost1) cost2=dcos(omicron(2,i)) @@ -17901,7 +18486,7 @@ chip1=chip(itypi) ctgt1=0.0d0 endif cosg_inv=1.0d0/cosg - if (itype(i-1,1).ne.ntyp1 .and. itype(i-2,1).ne.ntyp1) then +! 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) @@ -17913,7 +18498,7 @@ chip1=chip(itypi) +(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 +! endif ! write(iout,*) "just after,close to pi",dphi(j,3,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) @@ -17923,7 +18508,7 @@ chip1=chip(itypi) ! 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 +! 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) @@ -17941,7 +18526,7 @@ chip1=chip(itypi) write(iout,*) "just after",dphi(j,3,i),sing,dcosphi(j,3,i) #endif !#undef DEBUG - endif +! endif enddo endif enddo @@ -18366,7 +18951,7 @@ chip1=chip(itypi) end subroutine intcartderiv !----------------------------------------------------------------------------- subroutine checkintcartgrad - ! implicit real*8 (a-h,o-z) + ! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' #ifdef MPI include 'mpif.h' @@ -18527,7 +19112,7 @@ chip1=chip(itypi) ! q_measure.F !----------------------------------------------------------------------------- real(kind=8) function qwolynes(seg1,seg2,flag,seg3,seg4) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -18603,7 +19188,7 @@ chip1=chip(itypi) end function qwolynes !----------------------------------------------------------------------------- subroutine qwolynes_prim(seg1,seg2,flag,seg3,seg4) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -18716,7 +19301,7 @@ chip1=chip(itypi) end subroutine qwolynes_prim !----------------------------------------------------------------------------- subroutine qwol_num(seg1,seg2,flag,seg3,seg4) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.CHAIN' @@ -18763,7 +19348,7 @@ chip1=chip(itypi) !----------------------------------------------------------------------------- subroutine EconstrQ ! MD with umbrella_sampling using Wolyne's distance measure as a constraint -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CONTROL' ! include 'COMMON.VAR' @@ -18899,7 +19484,7 @@ chip1=chip(itypi) !----------------------------------------------------------------------------- subroutine dEconstrQ_num ! Calculating numerical dUconst/ddc and dUconst/ddx -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.CONTROL' ! include 'COMMON.VAR' @@ -19045,14 +19630,14 @@ chip1=chip(itypi) !EL external ran_number ! Local variables - integer :: i,j,k,l,lmax,p,pmax + integer :: i,j,k,l,lmax,p,pmax,countss real(kind=8) :: rmin,rmax real(kind=8) :: eij real(kind=8) :: d real(kind=8) :: wi,rij,tj,pj ! return - + countss=1 i=5 j=14 @@ -19099,14 +19684,14 @@ chip1=chip(itypi) dc_norm(k,nres+j)=dc(k,nres+j)/d enddo - call dyn_ssbond_ene(i,j,eij) + call dyn_ssbond_ene(i,j,eij,countss) enddo enddo call exit(1) return end subroutine check_energies !----------------------------------------------------------------------------- - subroutine dyn_ssbond_ene(resi,resj,eij) + subroutine dyn_ssbond_ene(resi,resj,eij,countss) ! implicit none ! Includes use calc_data @@ -19139,7 +19724,7 @@ chip1=chip(itypi) ! Local variables logical :: havebond - integer itypi,itypj + integer itypi,itypj,countss real(kind=8) :: rrij,ssd,deltat1,deltat2,deltat12,cosphi real(kind=8) :: sig0ij,ljd,sig,fac,e1,e2 real(kind=8),dimension(3) :: dcosom1,dcosom2 @@ -19437,9 +20022,9 @@ chip1=chip(itypi) ! endif !#endif !#endif - dyn_ssbond_ij(i,j)=eij - else if (.not.havebond .and. dyn_ssbond_ij(i,j).lt.1.0d300) then - dyn_ssbond_ij(i,j)=1.0d300 + dyn_ssbond_ij(countss)=eij + else if (.not.havebond .and. dyn_ssbond_ij(countss).lt.1.0d300) then + dyn_ssbond_ij(countss)=1.0d300 !#ifndef CLUST !#ifndef WHAM ! write(iout,'(a15,f12.2,f8.1,2i5)') @@ -19720,10 +20305,10 @@ chip1=chip(itypi) ! include 'COMMON.MD' ! Local variables real(kind=8) :: emin - integer :: i,j,imin,ierr + integer :: i,j,imin,ierr,k integer :: diff,allnss,newnss integer,dimension(maxdim) :: allflag,allihpb,alljhpb,& !(maxdim)(maxdim=(maxres-1)*(maxres-2)/2) - newihpb,newjhpb + newihpb,newjhpb,aliass logical :: found integer,dimension(0:nfgtasks) :: i_newnss integer,dimension(0:nfgtasks) :: displ @@ -19731,14 +20316,19 @@ chip1=chip(itypi) integer :: g_newnss allnss=0 + k=0 do i=1,nres-1 do j=i+1,nres - if (dyn_ssbond_ij(i,j).lt.1.0d300) then + if ((itype(i,1).eq.1).and.(itype(j,1).eq.1)) then + k=k+1 + if (dyn_ssbond_ij(k).lt.1.0d300) then allnss=allnss+1 allflag(allnss)=0 allihpb(allnss)=i alljhpb(allnss)=j - endif + aliass(allnss)=k + endif + endif enddo enddo @@ -19747,8 +20337,8 @@ chip1=chip(itypi) 1 emin=1.0d300 do i=1,allnss if (allflag(i).eq.0 .and. & - dyn_ssbond_ij(allihpb(i),alljhpb(i)).lt.emin) then - emin=dyn_ssbond_ij(allihpb(i),alljhpb(i)) + dyn_ssbond_ij(aliass(allnss)).lt.emin) then + emin=dyn_ssbond_ij(aliass(allnss)) imin=i endif enddo @@ -20371,14 +20961,18 @@ chip1=chip(itypi) end subroutine calctube2 !===================================================================================================================================== subroutine calcnano(Etube) - real(kind=8),dimension(3) :: vectube + use MD_data, only:totTafm + real(kind=8),dimension(3) :: vectube,cm 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 - + sc_aa_tube,sc_bb_tube,zmin,ztemp,zminact,tubezcenter,xi,yi,zi!,& +! vecsim,vectrue + real(kind=8) :: eps,sig,aa_tub_lip,bb_tub_lip + integer:: i,j,iti,r,ilol,ityp +! totTafm=2.0 Etube=0.0d0 + call to_box(tubecenter(1),tubecenter(2),tubecenter(3)) ! print *,itube_start,itube_end,"poczatek" do i=itube_start,itube_end enetube(i)=0.0d0 @@ -20391,43 +20985,17 @@ chip1=chip(itypi) !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 +! do j=-1,1 + xi=(c(1,i)+c(1,i+1))/2.0d0 + yi=(c(2,i)+c(2,i+1))/2.0d0 + zi=((c(3,i)+c(3,i+1))/2.0d0) + call to_box(xi,yi,zi) +! tubezcenter=totTafm*velNANOconst+tubecenter(3) - vectube(1)=vectube(1)-tubecenter(1) - vectube(2)=vectube(2)-tubecenter(2) - vectube(3)=vectube(3)-tubecenter(3) + vectube(1)=boxshift(xi-tubecenter(1),boxxsize) + vectube(2)=boxshift(yi-tubecenter(2),boxysize) + vectube(3)=boxshift(zi-tubecenter(3),boxzsize) !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) @@ -20472,7 +21040,7 @@ chip1=chip(itypi) !C fac=fac+faccav !C 667 continue endif - if (energy_dec) write(iout,*),i,rdiff,enetube(i),enecavtube(i) + if (energy_dec) write(iout,*),"ETUBE_PEP",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 @@ -20488,44 +21056,17 @@ chip1=chip(itypi) !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 - + xi=c(1,i+nres) + yi=c(2,i+nres) + zi=c(3,i+nres) + call to_box(xi,yi,zi) + tubezcenter=totTafm*velNANOconst+tubecenter(3) - xminact=dabs(vectube(1)-tubecenter(1)) - yminact=dabs(vectube(2)-tubecenter(2)) - zminact=dabs(vectube(3)-tubecenter(3)) + vectube(1)=boxshift(xi-tubecenter(1),boxxsize) + vectube(2)=boxshift(yi-tubecenter(2),boxysize) + vectube(3)=boxshift(zi-tubecenter(3),boxzsize) - 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 @@ -20575,15 +21116,92 @@ chip1=chip(itypi) 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) + if (energy_dec) write(iout,*),"ETUBE",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=ilipbond_start_tub,ilipbond_end_tub + ityp=itype(i,4) +! print *,"ilipbond_start",ilipbond_start,i,ityp + if (ityp.gt.ntyp_molec(4)) cycle +!C now calculate distance from center of tube and direction vectors + eps=lip_sig(ityp,18)*4.0d0 + sig=lip_sig(ityp,18) + aa_tub_lip=eps/(sig**12) + bb_tub_lip=eps/(sig**6) +! do j=-1,1 + xi=c(1,i) + yi=c(2,i) + zi=c(3,i) + call to_box(xi,yi,zi) +! tubezcenter=totTafm*velNANOconst+tubecenter(3) + + vectube(1)=boxshift(xi-tubecenter(1),boxxsize) + vectube(2)=boxshift(yi-tubecenter(2),boxysize) + vectube(3)=boxshift(zi-tubecenter(3),boxzsize) + +!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)=aa_tub_lip/rdiff6**2.0d0+bb_tub_lip/rdiff6 + Etube=Etube+enetube(i) +!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*aa_tub_lip/rdiff6- & + 6.0d0*bb_tub_lip)/rdiff6/rdiff + do j=1,3 + gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac + enddo + if (energy_dec) write(iout,*) "ETUBLIP",i,rdiff,enetube(i+nres) + enddo + + +!----------------------------------------------------------------------- + if (fg_rank.eq.0) then + if (velNANOconst.ne.0) then + do j=1,3 + cm(j)=0.0d0 + enddo + do i=1,inanomove + ilol=inanotab(i) + do j=1,3 + cm(j)=cm(j)+c(j,ilol) + enddo + enddo + do j=1,3 + cm(j)=cm(j)/inanomove + enddo + vecsim=velNANOconst*totTafm+distnanoinit + vectrue=cm(3)-tubecenter(3) + etube=etube+0.5d0*forcenanoconst*( vectrue-vecsim)**2 + fac=forcenanoconst*(vectrue-vecsim)/inanomove + do i=1,inanomove + ilol=inanotab(i) + gg_tube(3,ilol-1)=gg_tube(3,ilol-1)+fac + enddo + endif + endif ! do i=1,20 ! print *,"begin", i,"a" ! do r=1,10000 @@ -20793,17 +21411,40 @@ chip1=chip(itypi) ! SOUBROUTINE FOR AFM subroutine AFMvel(Eafmforce) use MD_data, only:totTafm - real(kind=8),dimension(3) :: diffafm + real(kind=8),dimension(3) :: diffafm,cbeg,cend real(kind=8) :: afmdist,Eafmforce - integer :: i + integer :: i,j !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 + cbeg=0.0d0 + cend=0.0d0 + if (afmbeg.eq.-1) then + do i=1,nbegafmmat + do j=1,3 + cbeg(j)=cbeg(j)+c(j,afmbegcentr(i))/nbegafmmat + enddo + enddo + else + do j=1,3 + cbeg(j)=c(j,afmend) + enddo + endif + if (afmend.eq.-1) then + do i=1,nendafmmat + do j=1,3 + cend(j)=cend(j)+c(j,afmendcentr(i))/nendafmmat + enddo + enddo + else + cend(j)=c(j,afmend) + endif + do i=1,3 - diffafm(i)=c(i,afmend)-c(i,afmbeg) + diffafm(i)=cend(i)-cbeg(i) afmdist=afmdist+diffafm(i)**2 enddo afmdist=dsqrt(afmdist) @@ -20811,14 +21452,36 @@ chip1=chip(itypi) Eafmforce=0.5d0*forceAFMconst & *(distafminit+totTafm*velAFMconst-afmdist)**2 !C Eafmforce=-forceAFMconst*(dist-distafminit) + if (afmend.eq.-1) then + do i=1,nendafmmat + do j=1,3 + gradafm(j,afmendcentr(i)-1)=-forceAFMconst* & + (distafminit+totTafm*velAFMconst-afmdist) & + *diffafm(j)/afmdist/nendafmmat + enddo + enddo + else do i=1,3 gradafm(i,afmend-1)=-forceAFMconst* & (distafminit+totTafm*velAFMconst-afmdist) & *diffafm(i)/afmdist + enddo + endif + if (afmbeg.eq.-1) then + do i=1,nbegafmmat + do j=1,3 + gradafm(i,afmbegcentr(i)-1)=forceAFMconst* & + (distafminit+totTafm*velAFMconst-afmdist) & + *diffafm(i)/afmdist + enddo + enddo + else + do i=1,3 gradafm(i,afmbeg-1)=forceAFMconst* & (distafminit+totTafm*velAFMconst-afmdist) & *diffafm(i)/afmdist enddo + endif ! print *,'AFM',Eafmforce,totTafm*velAFMconst,afmdist return end subroutine AFMvel @@ -20948,6 +21611,7 @@ chip1=chip(itypi) ! common /contacts1/ allocate(num_cont(0:nres+4)) !(maxres) +#ifndef NEWCORR allocate(jcont(maxconts,nres)) !(maxconts,maxres) allocate(facont(maxconts,nres)) @@ -20972,9 +21636,10 @@ chip1=chip(itypi) allocate(ees0plist(maxconts,nres)) !(maxconts,maxres) - allocate(num_cont_hb(nres)) !(maxres) allocate(jcont_hb(maxconts,nres)) +#endif + allocate(num_cont_hb(nres)) !(maxconts,maxres) ! common /rotat/ allocate(Ug(2,2,nres)) @@ -21049,9 +21714,9 @@ chip1=chip(itypi) allocate(sintab2(nres)) !(maxres) ! common /dipmat/ - allocate(a_chuj(2,2,maxconts,nres)) +! allocate(a_chuj(2,2,maxconts,nres)) !(2,2,maxconts,maxres)(maxconts=maxres/4) - allocate(a_chuj_der(2,2,3,5,maxconts,nres)) +! allocate(a_chuj_der(2,2,3,5,maxconts,nres)) !(2,2,3,5,maxconts,maxres)(maxconts=maxres/4) ! common /contdistrib/ allocate(ncont_sent(nres)) @@ -21059,8 +21724,12 @@ chip1=chip(itypi) allocate(iat_sent(nres)) !(maxres) +#ifndef NEWCORR + print *,"before iint_sent allocate" allocate(iint_sent(4,nres,nres)) allocate(iint_sent_local(4,nres,nres)) + print *,"after iint_sent allocate" +#endif !(4,maxres,maxres) allocate(iturn3_sent(4,0:nres+4)) allocate(iturn4_sent(4,0:nres+4)) @@ -21076,8 +21745,15 @@ chip1=chip(itypi) !---------------------- ! commom.deriv; ! common /derivat/ +#ifdef NEWCORR + print *,"before dcdv allocate" + allocate(dcdv(6,nres+2)) + allocate(dxdv(6,nres+2)) +#else + print *,"before dcdv allocate" allocate(dcdv(6,maxdim)) allocate(dxdv(6,maxdim)) +#endif !(6,maxdim) allocate(dxds(6,nres)) !(6,maxres) @@ -21142,9 +21818,19 @@ chip1=chip(itypi) allocate(gvdwpp_nucl(3,-1:nres)) allocate(gradpepcat(3,-1:nres)) allocate(gradpepcatx(3,-1:nres)) + allocate(gradpepmart(3,-1:nres)) + allocate(gradpepmartx(3,-1:nres)) allocate(gradcatcat(3,-1:nres)) allocate(gradnuclcat(3,-1:nres)) allocate(gradnuclcatx(3,-1:nres)) + allocate(gradlipbond(3,-1:nres)) + allocate(gradlipang(3,-1:nres)) + allocate(gradliplj(3,-1:nres)) + allocate(gradlipelec(3,-1:nres)) + allocate(gradcattranc(3,-1:nres)) + allocate(gradcattranx(3,-1:nres)) + allocate(gradcatangx(3,-1:nres)) + allocate(gradcatangc(3,-1:nres)) !(3,maxres) allocate(grad_shield_side(3,maxcontsshi,-1:nres)) allocate(grad_shield_loc(3,maxcontsshi,-1:nres)) @@ -21264,11 +21950,11 @@ chip1=chip(itypi) !el integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane ! common /dyn_ssbond/ ! and side-chain vectors in theta or phi. - allocate(dyn_ssbond_ij(0:nres+4,0:nres+4)) + allocate(dyn_ssbond_ij(10000)) !(maxres,maxres) ! do i=1,nres ! do j=i+1,nres - dyn_ssbond_ij(:,:)=1.0d300 + dyn_ssbond_ij(:)=1.0d300 ! enddo ! enddo @@ -21327,6 +22013,7 @@ chip1=chip(itypi) allocate(uygrad(3,3,2,nres)) allocate(uzgrad(3,3,2,nres)) !(3,3,2,maxres) + print *,"before all 300" ! allocateion of lists JPRDLA allocate(newcontlistppi(300*nres)) allocate(newcontlistscpi(350*nres)) @@ -21334,6 +22021,32 @@ chip1=chip(itypi) allocate(newcontlistppj(300*nres)) allocate(newcontlistscpj(350*nres)) allocate(newcontlistj(300*nres)) + allocate(newcontlistmartpi(300*nres)) + allocate(newcontlistmartpj(300*nres)) + allocate(newcontlistmartsci(300*nres)) + allocate(newcontlistmartscj(300*nres)) + + allocate(newcontlistcatsctrani(300*nres)) + allocate(newcontlistcatsctranj(300*nres)) + allocate(newcontlistcatptrani(300*nres)) + allocate(newcontlistcatptranj(300*nres)) + allocate(newcontlistcatscnormi(300*nres)) + allocate(newcontlistcatscnormj(300*nres)) + allocate(newcontlistcatpnormi(300*nres)) + allocate(newcontlistcatpnormj(300*nres)) + allocate(newcontlistcatcatnormi(900*nres)) + allocate(newcontlistcatcatnormj(900*nres)) + + allocate(newcontlistcatscangi(300*nres)) + allocate(newcontlistcatscangj(300*nres)) + allocate(newcontlistcatscangfi(300*nres)) + allocate(newcontlistcatscangfj(300*nres)) + allocate(newcontlistcatscangfk(300*nres)) + allocate(newcontlistcatscangti(300*nres)) + allocate(newcontlistcatscangtj(300*nres)) + allocate(newcontlistcatscangtk(300*nres)) + allocate(newcontlistcatscangtl(300*nres)) + return end subroutine alloc_ener_arrays @@ -21353,8 +22066,22 @@ chip1=chip(itypi) 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 + + if (itype(i-1,2).eq.ntyp1_molec(2)& + .and.itype(i,2).eq.ntyp1_molec(2)) cycle + if (itype(i-1,2).eq.ntyp1_molec(2)& + .or. itype(i,2).eq.ntyp1_molec(2)) 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) & +!C *dc(j,i-1)/vbld(i) +!C enddo +!C if (energy_dec) write(iout,*) & +!C "estr1",i,gnmr1(vbld(i),-1.0d0,distchainmax) + diff = vbld(i)-vbldpDUM + else + diff = vbld(i)-vbldp0_nucl + endif ! estr1=estr1+gnmr1(vbld(i),-1.0d0,distchainmax) ! do j=1,3 ! gradb(j,i-1)=gnmr1prim(vbld(i),-1.0d0,distchainmax) @@ -21364,7 +22091,6 @@ chip1=chip(itypi) ! & "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 @@ -21615,7 +22341,7 @@ chip1=chip(itypi) end subroutine ebend_nucl !---------------------------------------------------- subroutine etor_nucl(etors_nucl) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.VAR' ! include 'COMMON.GEO' @@ -22394,7 +23120,7 @@ chip1=chip(itypi) 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,*) "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) @@ -22749,7 +23475,7 @@ chip1=chip(itypi) 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) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.DERIV' @@ -22824,7 +23550,7 @@ chip1=chip(itypi) !------------------------------------------------------------------------- real(kind=8) function ehbcorr3_nucl(i,j,k,l,jj,kk,coeffp,coeffm) -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.IOUNITS' ! include 'COMMON.DERIV' @@ -22945,16 +23671,19 @@ chip1=chip(itypi) !c------------------------------------------------------------------------------ #endif subroutine ecatcat(ecationcation) - integer :: i,j,itmp,xshift,yshift,zshift,subchap,k,itypi,itypj + use MD_data, only: t_bath + integer :: i,j,itmp,xshift,yshift,zshift,subchap,k,itypi,itypj,irdiff,& + ii real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,& r7,r4,ecationcation,k0,rcal,aa,bb,sslipi,ssgradlipi,sslipj,ssgradlipj - real(kind=8) xj_temp,yj_temp,zj_temp,xj_safe,yj_safe,zj_safe, & + 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) :: awat,bwat,cwat,dwat,sss2min2,sss2mingrad2,rdiff,ewater real(kind=8),dimension(3) ::dEvan1Cmcat,dEvan2Cmcat,dEeleccat,& gg,r ecationcation=0.0d0 - if (nres_molec(5).eq.0) return + if (nres_molec(5).le.1) return rcat0=3.472 epscalc=0.05 r06 = rcat0**6 @@ -22962,12 +23691,15 @@ chip1=chip(itypi) ! k0 = 332.0*(2.0*2.0)/80.0 itmp=0 - do i=1,4 - itmp=itmp+nres_molec(i) - enddo -! write(iout,*) "itmp",itmp - do i=itmp+1,itmp+nres_molec(5)-1 - +! do i=1,4 +! itmp=itmp+nres_molec(i) +! enddo +! write(iout,*) "itmp",g_listcatcatnorm_start, g_listcatcatnorm_end +! do i=itmp+1,itmp+nres_molec(5)-1 + do ii=g_listcatcatnorm_start, g_listcatcatnorm_end + i=newcontlistcatcatnormi(ii) + j=newcontlistcatcatnormj(ii) + xi=c(1,i) yi=c(2,i) zi=c(3,i) @@ -22975,7 +23707,7 @@ chip1=chip(itypi) itypi=itype(i,5) call to_box(xi,yi,zi) call lipid_layer(xi,yi,zi,sslipi,ssgradlipi) - do j=i+1,itmp+nres_molec(5) +! do j=i+1,itmp+nres_molec(5) itypj=itype(j,5) ! print *,i,j,itypi,itypj k0 = 332.0*(ichargecat(itypi)*ichargecat(itypj))/80.0 @@ -22994,6 +23726,10 @@ chip1=chip(itypi) zj=boxshift(zj-zi,boxzsize) rcal =xj**2+yj**2+zj**2 ract=sqrt(rcal) + if ((itypi.gt.1).or.(itypj.gt.1)) then + if (sss2min2.eq.0.0d0) cycle + sss2min2=sscale2(ract,12.0d0,1.0d0) + sss2mingrad2=sscagrad2(ract,12.0d0,1.0d0) ! rcat0=3.472 ! epscalc=0.05 ! r06 = rcat0**6 @@ -23014,15 +23750,45 @@ chip1=chip(itypi) 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) + gradcatcat(k,i)=gradcatcat(k,i)-(gg(k)*sss2min2+(Evan1cat+Evan2cat+Eeleccat)*sss2mingrad2) + gradcatcat(k,j)=gradcatcat(k,j)+gg(k)*sss2min2+(Evan1cat+Evan2cat+Eeleccat)*sss2mingrad2 enddo - if (energy_dec) write (iout,*) i,j,Evan1cat,Evan2cat,Eeleccat,& + if (energy_dec) write (iout,*) "ecatcat",i,j,Evan1cat,Evan2cat,Eeleccat,& r012,rcal**6,ichargecat(itypi)*ichargecat(itypj) ! write(iout,*) "ecatcat",i,j, ecationcation,xj,yj,zj - ecationcation=ecationcation+Evan1cat+Evan2cat+Eeleccat - enddo + ecationcation=ecationcation+(Evan1cat+Evan2cat+Eeleccat)*sss2min2 + else !this is water part and other non standard molecules + + sss2min2=sscale2(ract,10.0d0,1.0d0)! cutoff for water interaction is 15A + if (sss2min2.eq.0.0d0) cycle + sss2mingrad2=sscagrad2(ract,10.0d0,1.0d0) + irdiff=int((ract-2.06d0)*50.0d0)+1 + + rdiff=ract-((irdiff-1)*0.02d0+2.06d0) + if (irdiff.le.0) then + irdiff=0 + rdiff=ract + endif +! print *,rdiff,ract,irdiff,sss2mingrad2 + awat=awaterenta(irdiff)-awaterentro(irdiff)*t_bath/1000.0d0 + bwat=bwaterenta(irdiff)-bwaterentro(irdiff)*t_bath/1000.0d0 + cwat=cwaterenta(irdiff)-cwaterentro(irdiff)*t_bath/1000.0d0 + dwat=dwaterenta(irdiff)-dwaterentro(irdiff)*t_bath/1000.0d0 + r(1)=xj + r(2)=yj + r(3)=zj + + ewater=awat+bwat*rdiff+cwat*rdiff*rdiff+dwat*rdiff*rdiff*rdiff + ecationcation=ecationcation+ewater*sss2min2 + do k=1,3 + gg(k)=(bwat+2.0d0*cwat*rdiff+dwat*3.0d0*rdiff*rdiff)*r(k)/ract + gradcatcat(k,i)=gradcatcat(k,i)-gg(k)*sss2min2-sss2mingrad2*ewater*r(k)/ract + gradcatcat(k,j)=gradcatcat(k,j)+gg(k)*sss2min2+sss2mingrad2*ewater*r(k)/ract + enddo + if (energy_dec) write(iout,'(2f8.2,f10.2,2i5)') rdiff,ract,ecationcation,i,j + endif ! end water enddo +! enddo return end subroutine ecatcat !--------------------------------------------------------------------------- @@ -23040,7 +23806,7 @@ chip1=chip(itypi) real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& dist_temp, dist_init,ssgradlipi,ssgradlipj, & sslipi,sslipj,faclip,alpha_sco - integer :: ii + integer :: ii,ki real(kind=8) :: fracinbuf real (kind=8) :: escpho real (kind=8),dimension(4):: ener @@ -23072,7 +23838,10 @@ chip1=chip(itypi) enddo ! go to 17 ! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization - do i=ibond_start,ibond_end +! do i=ibond_start,ibond_end + do ki=g_listcatscnorm_start,g_listcatscnorm_end + i=newcontlistcatscnormi(ki) + j=newcontlistcatscnormj(ki) ! print *,"I am in EVDW",i itypi=iabs(itype(i,1)) @@ -23089,7 +23858,7 @@ chip1=chip(itypi) dyi=dc_norm(2,nres+i) dzi=dc_norm(3,nres+i) dsci_inv=vbld_inv(i+nres) - do j=itmp+1,itmp+nres_molec(5) +! do j=itmp+1,itmp+nres_molec(5) ! Calculate SC interaction energy. itypj=iabs(itype(j,5)) @@ -23114,6 +23883,9 @@ chip1=chip(itypi) zj=boxshift(zj-zi,boxzsize) ! write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize + dxj=0.0 + dyj=0.0 + dzj=0.0 ! dxj = dc_norm( 1, nres+j ) ! dyj = dc_norm( 2, nres+j ) ! dzj = dc_norm( 3, nres+j ) @@ -23138,6 +23910,7 @@ chip1=chip(itypi) ! chis2 = chis(itypj,itypi) chis12 = chis1 * chis2 sig1 = sigmap1cat(itypi,itypj) + sig2=0.0d0 ! sig2 = sigmap2(itypi,itypj) ! alpha factors from Fcav/Gcav b1cav = alphasurcat(1,itypi,itypj) @@ -23222,6 +23995,11 @@ chip1=chip(itypi) ! rij holds 1/(distance of Calpha atoms) rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) rij = dsqrt(rrij) + sss_ele_cut=sscale_ele(1.0d0/(rij)) + sss_ele_grad=sscagrad_ele(1.0d0/(rij)) +! print *,sss_ele_cut,sss_ele_grad,& +! 1.0d0/(rij),r_cut_ele,rlamb_ele + if (sss_ele_cut.le.0.0) cycle 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 @@ -23272,15 +24050,15 @@ chip1=chip(itypi) ! END IF !#else evdw = evdw & - + evdwij + + evdwij*sss_ele_cut !#endif c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 fac = -expon * (c1 + evdwij) * rij_shift sigder = fac * sigder ! Calculate distance derivative - gg(1) = fac - gg(2) = fac - gg(3) = fac + gg(1) = fac*sss_ele_cut+evdwij*sss_ele_grad + gg(2) = fac*sss_ele_cut+evdwij*sss_ele_grad + gg(3) = fac*sss_ele_cut+evdwij*sss_ele_grad ! print *,"GG(1),distance grad",gg(1) fac = chis1 * sqom1 + chis2 * sqom2 & - 2.0d0 * chis12 * om1 * om2 * om12 @@ -23299,8 +24077,9 @@ chip1=chip(itypi) dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf)) dbot = 12.0d0 * b4cav * bat * Lambf - dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow - + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+& + Fcav*sss_ele_grad + Fcav=Fcav*sss_ele_cut dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif)) dbot = 12.0d0 * b4cav * bat * Chif eagle = Lambf * pom @@ -23340,61 +24119,47 @@ chip1=chip(itypi) isel = iabs(Qi) + 1 ! ion is always charged so iabs(Qj) ! print *,i,itype(i,1),isel IF (isel.eq.0) THEN -!c! No charges - do nothing eheadtail = 0.0d0 - ELSE IF (isel.eq.1) THEN -!c! Nonpolar-charge interactions if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then Qi=Qi*2 Qij=Qij*2 endif - CALL enq_cat(epol) eheadtail = epol -! eheadtail = 0.0d0 - ELSE IF (isel.eq.3) THEN -!c! Dipole-charge interactions if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then Qi=Qi*2 Qij=Qij*2 endif -! write(iout,*) "KURWA0",d1 - CALL edq_cat(ecl, elj, epol) eheadtail = ECL + elj + epol -! eheadtail = 0.0d0 - ELSE IF ((isel.eq.2)) THEN - -!c! Same charge-charge interaction ( +/+ or -/- ) if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then Qi=Qi*2 Qij=Qij*2 endif - CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj) eheadtail = ECL + Egb + Epol + Fisocav + Elj -! eheadtail = 0.0d0 - -! ELSE IF ((isel.eq.2.and. & -! iabs(Qi).eq.1).and. & -! nstate(itypi,itypj).ne.1) THEN -!c! Different charge-charge interaction ( +/- or -/+ ) -! if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then -! Qi=Qi*2 -! Qij=Qij*2 -! endif -! if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then -! Qj=Qj*2 -! Qij=Qij*2 -! endif -! -! CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad) END IF ! this endif ends the "catch the gly-gly" at the beggining of Fcav - else - write(iout,*) "not yet implemented",j,itype(j,5) + else ! here is water and other molecules + isel = iabs(Qi)+2 +! isel=2 +! if (isel.eq.4) isel=2 + if (isel.eq.2) then + eheadtail = 0.0d0 + else if (isel.eq.3) then + if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then + Qi=Qi*2 + Qij=Qij*2 + endif + call eqd_cat(ecl,elj,epol) + eheadtail = ECL + elj + epol + else if (isel.eq.4) then + call edd_cat(ecl) + eheadtail = ECL + endif +! write(iout,*) "not yet implemented",j,itype(j,5) endif !! endif ! turn off electrostatic evdw = evdw + Fcav + eheadtail @@ -23410,6 +24175,8 @@ chip1=chip(itypi) 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& Equad,evdwij+Fcav+eheadtail,evdw ! evdw = evdw + Fcav + eheadtail + if (energy_dec) write(iout,*) "FCAV", & + sig1,sig2,b1cav,b2cav,b3cav,b4cav ! print *,"before sc_grad_cat", i,j, gradpepcat(1,j) ! iF (nstate(itypi,itypj).eq.1) THEN CALL sc_grad_cat @@ -23419,14 +24186,18 @@ chip1=chip(itypi) !c!------------------------------------------------------------------- !c! NAPISY KONCOWE END DO ! j - END DO ! i +! END DO ! i !c write (iout,*) "Number of loop steps in EGB:",ind !c energy_dec=.false. ! print *,"EVDW KURW",evdw,nres !!! return 17 continue ! go to 23 - do i=ibond_start,ibond_end +! do i=ibond_start,ibond_end + + do ki=g_listcatpnorm_start,g_listcatpnorm_end + i=newcontlistcatpnormi(ki) + j=newcontlistcatpnormj(ki) ! print *,"I am in EVDW",i itypi=10 ! the peptide group parameters are for glicine @@ -23442,7 +24213,7 @@ chip1=chip(itypi) dyi=dc_norm(2,i) dzi=dc_norm(3,i) dsci_inv=vbld_inv(i+1)/2.0 - do j=itmp+1,itmp+nres_molec(5) +! do j=itmp+1,itmp+nres_molec(5) ! Calculate SC interaction energy. itypj=iabs(itype(j,5)) @@ -23484,6 +24255,7 @@ chip1=chip(itypi) ! chis2 = chis(itypj,itypi) chis12 = chis1 * chis2 sig1 = sigmap1cat(itypi,itypj) + sig2=0.0 ! sig2 = sigmap2(itypi,itypj) ! alpha factors from Fcav/Gcav b1cav = alphasurcat(1,itypi,itypj) @@ -23566,15 +24338,22 @@ chip1=chip(itypi) dCAVdOM1 = 0.0d0 dCAVdOM2 = 0.0d0 dCAVdOM12 = 0.0d0 - dscj_inv = vbld_inv(j+nres) + dscj_inv = 0.0d0 ! 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) + sss_ele_cut=sscale_ele(1.0d0/(rij)) + sss_ele_grad=sscagrad_ele(1.0d0/(rij)) +! print *,sss_ele_cut,sss_ele_grad,& +! 1.0d0/(rij),r_cut_ele,rlamb_ele + if (sss_ele_cut.le.0.0) cycle 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 + om2=0.0d0 + om12=0.0d0 sqom1 = om1 * om1 sqom2 = om2 * om2 sqom12 = om12 * om12 @@ -23618,15 +24397,15 @@ chip1=chip(itypi) ! END IF !#else evdw = evdw & - + evdwij + + evdwij*sss_ele_cut !#endif c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 fac = -expon * (c1 + evdwij) * rij_shift sigder = fac * sigder ! Calculate distance derivative - gg(1) = fac - gg(2) = fac - gg(3) = fac + gg(1) = fac*sss_ele_cut+evdwij*sss_ele_grad + gg(2) = fac*sss_ele_cut+evdwij*sss_ele_grad + gg(3) = fac*sss_ele_cut+evdwij*sss_ele_grad fac = chis1 * sqom1 + chis2 * sqom2 & - 2.0d0 * chis12 * om1 * om2 * om12 @@ -23647,20 +24426,24 @@ chip1=chip(itypi) dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf)) dbot = 12.0d0 * b4cav * bat * Lambf - dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow - + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+& + Fcav*sss_ele_grad + Fcav=Fcav*sss_ele_cut dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif)) dbot = 12.0d0 * b4cav * 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) dCAVdOM1 = dFdL * ( dFdOM1 ) - dCAVdOM2 = dFdL * ( dFdOM2 ) - dCAVdOM12 = dFdL * ( dFdOM12 ) +! dCAVdOM2 = dFdL * ( dFdOM2 ) +! dCAVdOM12 = dFdL * ( dFdOM12 ) + dCAVdOM2=0.0d0 + dCAVdOM12=0.0d0 DO k= 1, 3 ertail(k) = Rtail_distance(k)/Rtail @@ -23695,8 +24478,11 @@ chip1=chip(itypi) ! eheadtail = 0.0d0 else !HERE WATER and other types of molecules solvents will be added - write(iout,*) "not yet implemented" +! write(iout,*) "not yet implemented" + CALL edd_cat_pep(ecl) + eheadtail=ecl ! CALL edd_cat_pep +! eheadtail=0.0d0 endif evdw = evdw + Fcav + eheadtail ! if (evdw.gt.1.0d6) then @@ -23717,7 +24503,7 @@ chip1=chip(itypi) !c!------------------------------------------------------------------- !c! NAPISY KONCOWE END DO ! j - END DO ! i +! END DO ! i !c write (iout,*) "Number of loop steps in EGB:",ind !c energy_dec=.false. ! print *,"EVDW KURW",evdw,nres @@ -23734,7 +24520,7 @@ chip1=chip(itypi) ! use comm_momo integer i,j,k,subchap,itmp,inum real(kind=8) :: xi,yi,zi,xj,yj,zj,ract,rcat0,epscalc,r06,r012,& - r7,r4,ecationcation + r7,r4 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, & @@ -23767,6 +24553,7 @@ chip1=chip(itypi) ! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization do i=ibond_start,ibond_end ! 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)) @@ -24289,7 +25076,9 @@ chip1=chip(itypi) do i=1,4 itmp=itmp+nres_molec(i) enddo - do i=iatsc_s_nucl,iatsc_e_nucl +! print *,nres_molec(2),"nres2" + do i=ibond_nucl_start,ibond_nucl_end +! do i=iatsc_s_nucl,iatsc_e_nucl if ((itype(i,2).eq.ntyp1_molec(2))) cycle ! leave dummy atoms xi=(c(1,i+nres)) yi=(c(2,i+nres)) @@ -24304,6 +25093,7 @@ chip1=chip(itypi) yj=c(2,j) zj=c(3,j) call to_box(xj,yj,zj) +! print *,i,j,itmp ! write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,xj,yj,zj ! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) ! aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 & @@ -24481,7 +25271,7 @@ chip1=chip(itypi) !----------------------------------------------------------------------------- subroutine eprot_sc_base(escbase) use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -24559,6 +25349,7 @@ chip1=chip(itypi) ! BetaT = 1.0d0 / (298.0d0 * Rb) ! Gay-berne var's sig0ij = sigma_scbase( itypi,itypj ) + if (sig0ij.lt.0.2) print *,"KURWA",sig0ij,itypi,itypj chi1 = chi_scbase( itypi, itypj,1 ) chi2 = chi_scbase( itypi, itypj,2 ) ! chi1=0.0d0 @@ -24684,8 +25475,10 @@ chip1=chip(itypi) 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 + sparrow=dsqrt(sig1**2.0d0 + sig2**2.0d0) + if (b1.eq.0.0d0) sparrow=1.0d0 + sparrow = 1.0d0 / sparrow +! write (*,*) "sparrow = ", sparrow,sig1,sig2,b1 Chif = 1.0d0/rij * sparrow ChiLambf = Chif * Lambf eagle = dsqrt(ChiLambf) @@ -24942,6 +25735,9 @@ chip1=chip(itypi) endif ! print *,i,j,evdwij,epol,Fcav,ECL escbase=escbase+evdwij+epol+Fcav+ECL + if (energy_dec) write (iout,'(a22,2i5,4f8.3,f16.3)'), & + "escbase:evdw,pol,cav,CL",i,j,evdwij,epol,Fcav,ECL,escbase + if (energy_dec) write (iout,*) "evdwij,", evdwij, 1.0/rij, sig, sig0ij call sc_grad_scbase enddo enddo @@ -24992,6 +25788,7 @@ chip1=chip(itypi) 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 @@ -25305,6 +26102,8 @@ chip1=chip(itypi) END DO ! print *,i,j,evdwij,Fcav,ECL,"vdw,cav,ecl" epepbase=epepbase+evdwij+Fcav+ECL + if (energy_dec) write (iout,'(a22,2i5,4f8.3,f16.3)'), & + "epepbase:evdw,pol,cav,CL",i,j,evdwij,epol,Fcav,ECL,epepbase call sc_grad_pepbase enddo enddo @@ -25368,7 +26167,7 @@ chip1=chip(itypi) END SUBROUTINE sc_grad_pepbase subroutine eprot_sc_phosphate(escpho) use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -25846,7 +26645,7 @@ chip1=chip(itypi) END SUBROUTINE sc_grad_scpho subroutine eprot_pep_phosphate(epeppho) use calc_data -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -26035,6 +26834,9 @@ chip1=chip(itypi) 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 + if (energy_dec) write (iout,'(a22,2i5,4f8.3,f16.3)'), & + "epeppho:evdw,pol,cav,CL",i,j,evdwij,epol,Fcav,ECL,epeppho + epeppho=epeppho+evdwij+Fcav+ECL ! print *,i,j,evdwij,Fcav,ECL,rij_shift enddo @@ -26044,7 +26846,7 @@ chip1=chip(itypi) subroutine emomo(evdw) use calc_data use comm_momo -! implicit real*8 (a-h,o-z) +! implicit real(kind=8) (a-h,o-z) ! include 'DIMENSIONS' ! include 'COMMON.GEO' ! include 'COMMON.VAR' @@ -26059,13 +26861,13 @@ chip1=chip(itypi) ! include 'COMMON.SBRIDGE' logical :: lprn !el local variables - integer :: iint,itypi1,subchap,isel + integer :: iint,itypi1,subchap,isel,countss real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi real(kind=8) :: evdw,aa,bb real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& dist_temp, dist_init,ssgradlipi,ssgradlipj, & sslipi,sslipj,faclip,alpha_sco - integer :: ii + integer :: ii,icont real(kind=8) :: fracinbuf real (kind=8) :: escpho real (kind=8),dimension(4):: ener @@ -26084,9 +26886,14 @@ chip1=chip(itypi) evdw=0.0d0 eps_out=80.0d0 sss_ele_cut=1.0d0 + countss=0 ! print *,"EVDW KURW",evdw,nres - do i=iatsc_s,iatsc_e +! do i=iatsc_s,iatsc_e ! print *,"I am in EVDW",i + do icont=g_listscsc_start,g_listscsc_end + i=newcontlisti(icont) + j=newcontlistj(icont) + itypi=iabs(itype(i,1)) ! if (i.ne.47) cycle if (itypi.eq.ntyp1) cycle @@ -26108,11 +26915,11 @@ chip1=chip(itypi) ! ! Calculate SC interaction energy. ! - do iint=1,nint_gr(i) - do j=istart(i,iint),iend(i,iint) +! do iint=1,nint_gr(i) +! do j=istart(i,iint),iend(i,iint) ! print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint) IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN - call dyn_ssbond_ene(i,j,evdwij) + call dyn_ssbond_ene(i,j,evdwij,countss) evdw=evdw+evdwij if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)') & 'evdw',i,j,evdwij,' ss' @@ -26161,6 +26968,9 @@ chip1=chip(itypi) xj=boxshift(xj-xi,boxxsize) yj=boxshift(yj-yi,boxysize) zj=boxshift(zj-zi,boxzsize) + Rreal(1)=xj + Rreal(2)=yj + Rreal(3)=zj dxj = dc_norm( 1, nres+j ) dyj = dc_norm( 2, nres+j ) dzj = dc_norm( 3, nres+j ) @@ -26213,11 +27023,14 @@ chip1=chip(itypi) ctail(k,1)=c(k,i+nres)-dtail(1,itypi,itypj)*dc_norm(k,nres+i) ctail(k,2)=c(k,j+nres)-dtail(2,itypi,itypj)*dc_norm(k,nres+j) END DO + call to_box (ctail(1,1),ctail(2,1),ctail(3,1)) + call to_box (ctail(1,2),ctail(2,2),ctail(3,2)) + !c! tail distances will be themselves usefull elswhere !c1 (in Gcav, for example) - Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 ) - Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 ) - Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 ) + Rtail_distance(1)=boxshift(ctail( 1, 2 ) - ctail( 1,1 ),boxxsize) + Rtail_distance(2)=boxshift(ctail( 2, 2 ) - ctail( 2,1 ),boxysize) + Rtail_distance(3)=boxshift(ctail( 3, 2 ) - ctail( 3,1 ),boxzsize) Rtail = dsqrt( & (Rtail_distance(1)*Rtail_distance(1)) & + (Rtail_distance(2)*Rtail_distance(2)) & @@ -26235,11 +27048,26 @@ chip1=chip(itypi) ! see unres publications for very informative images chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres) -! distance +! distance + enddo + if (energy_dec) write(iout,*) "before",chead(1,1),chead(2,1),chead(3,1) + if (energy_dec) write(iout,*) "before",chead(1,2),chead(2,2),chead(3,2) + call to_box (chead(1,1),chead(2,1),chead(3,1)) + call to_box (chead(1,2),chead(2,2),chead(3,2)) + +!c! head distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + if (energy_dec) write(iout,*) "after",chead(1,1),chead(2,1),chead(3,1) + if (energy_dec) write(iout,*) "after",chead(1,2),chead(2,2),chead(3,2) + + Rhead_distance(1)=boxshift(chead( 1, 2 ) - chead( 1,1 ),boxxsize) + Rhead_distance(2)=boxshift(chead( 2, 2 ) - chead( 2,1 ),boxysize) + Rhead_distance(3)=boxshift(chead( 3, 2 ) - chead( 3,1 ),boxzsize) + if (energy_dec) write(iout,*) "after,rdi",(Rhead_distance(k),k=1,3) ! 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 +! 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)) & @@ -26269,6 +27097,14 @@ chip1=chip(itypi) ! rij holds 1/(distance of Calpha atoms) rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj) rij = dsqrt(rrij) + sss_ele_cut=sscale_ele(1.0d0/(rij)) + sss_ele_grad=sscagrad_ele(1.0d0/(rij)) +! sss_ele_cut=1.0d0 +! sss_ele_grad=0.0d0 +! print *,sss_ele_cut,sss_ele_grad,& +! 1.0d0/(rij),r_cut_ele,rlamb_ele + if (sss_ele_cut.le.0.0) cycle + !---------------------------- CALL sc_angular ! this should be in elgrad_init but om's are calculated by sc_angular @@ -26310,7 +27146,7 @@ chip1=chip(itypi) ! END IF !#else evdw = evdw & - + evdwij + + evdwij*sss_ele_cut !#endif c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 @@ -26318,9 +27154,9 @@ chip1=chip(itypi) sigder = fac * sigder ! fac = rij * fac ! Calculate distance derivative - gg(1) = fac - gg(2) = fac - gg(3) = fac + gg(1) = fac*sss_ele_cut + gg(2) = fac*sss_ele_cut + gg(3) = fac*sss_ele_cut ! if (b2.gt.0.0) then fac = chis1 * sqom1 + chis2 * sqom2 & - 2.0d0 * chis12 * om1 * om2 * om12 @@ -26345,8 +27181,7 @@ chip1=chip(itypi) dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf)) dbot = 12.0d0 * b4cav * bat * Lambf - dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow - + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif)) dbot = 12.0d0 * b4cav * bat * Chif eagle = Lambf * pom @@ -26373,26 +27208,33 @@ chip1=chip(itypi) !c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) gvdwx(k,i) = gvdwx(k,i) & - - (( dFdR + gg(k) ) * pom) + - (( dFdR + gg(k) ) * pom)& + -sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij) !c! & - ( dFdR * pom ) pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres)) gvdwx(k,j) = gvdwx(k,j) & - + (( dFdR + gg(k) ) * pom) + + (( dFdR + gg(k) ) * pom) & + +sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij) + !c! & + ( dFdR * pom ) gvdwc(k,i) = gvdwc(k,i) & - - (( dFdR + gg(k) ) * ertail(k)) + - (( dFdR + gg(k) ) * ertail(k)) & + -sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij) + !c! & - ( dFdR * ertail(k)) gvdwc(k,j) = gvdwc(k,j) & - + (( dFdR + gg(k) ) * ertail(k)) + + (( dFdR + gg(k) ) * ertail(k)) & + +sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij) + !c! & + ( dFdR * ertail(k)) gg(k) = 0.0d0 ! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) ! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) END DO - + !c! Compute head-head and head-tail energies for each state @@ -26408,6 +27250,10 @@ chip1=chip(itypi) ! endif ! isel=0 +! if (isel.eq.2) isel=0 +! if (isel.eq.3) isel=0 +! if (iabs(Qj).eq.1) isel=0 +! nstate(itypi,itypj)=1 IF (isel.eq.0) THEN !c! No charges - do nothing eheadtail = 0.0d0 @@ -26510,7 +27356,7 @@ chip1=chip(itypi) CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad) END IF END IF ! this endif ends the "catch the gly-gly" at the beggining of Fcav - evdw = evdw + Fcav + eheadtail + evdw = evdw + Fcav*sss_ele_cut + eheadtail*sss_ele_cut IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') & restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& @@ -26523,8 +27369,8 @@ chip1=chip(itypi) END IF !c!------------------------------------------------------------------- !c! NAPISY KONCOWE - END DO ! j - END DO ! iint + ! END DO ! j + !END DO ! iint END DO ! i !c write (iout,*) "Number of loop steps in EGB:",ind !c energy_dec=.false. @@ -26537,7 +27383,7 @@ chip1=chip(itypi) use calc_data use comm_momo real (kind=8) :: facd3, facd4, federmaus, adler,& - Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap + Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap,sgrad ! integer :: k !c! Epol and Gpol analytical parameters alphapol1 = alphapol(itypi,itypj) @@ -26576,7 +27422,7 @@ chip1=chip(itypi) !c! Coulomb electrostatic interaction Ecl = (332.0d0 * Qij) / Rhead !c! derivative of Ecl is Gcl... - dGCLdR = (-332.0d0 * Qij ) / Rhead_sq + dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut dGCLdOM1 = 0.0d0 dGCLdOM2 = 0.0d0 dGCLdOM12 = 0.0d0 @@ -26592,7 +27438,7 @@ chip1=chip(itypi) -(332.0d0 * Qij *& (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb ) - dGGBdR = dGGBdFGB * dFGBdR + dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut !c!------------------------------------------------------------------- !c! Fisocav - isotropic cavity creation term !c! or "how much energy it costs to put charged head in water" @@ -26613,7 +27459,7 @@ chip1=chip(itypi) !c! Derivative of Fisocav is GCV... dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2) dbot = 12.0d0 * al4 * pom ** 11.0d0 - dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig + dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut !c!------------------------------------------------------------------- !c! Epol !c! Polarization energy - charged heads polarize hydrophobic "neck" @@ -26640,9 +27486,9 @@ chip1=chip(itypi) * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 ) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))& * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 ) - dPOLdR1 = dPOLdFGB1 * dFGBdR1 + dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut !c! dPOLdR1 = 0.0d0 - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 @@ -26655,7 +27501,7 @@ chip1=chip(itypi) Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) !c! derivative of Elj is Glj dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))& - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut !c!------------------------------------------------------------------- !c! Return the results !c! These things do the dRdX derivatives, that is @@ -26685,7 +27531,7 @@ chip1=chip(itypi) facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) condor = (erhead_tail(k,2) + & facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres))) - + sgrad=(Ecl+Egb+Epol+Fisocav+Elj)*sss_ele_grad*rreal(k)*rij pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) gvdwx(k,i) = gvdwx(k,i) & - dGCLdR * pom& @@ -26694,14 +27540,14 @@ chip1=chip(itypi) - dPOLdR1 * hawk& - dPOLdR2 * (erhead_tail(k,2)& -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))& - - dGLJdR * pom + - dGLJdR * pom-sgrad pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom& + dGGBdR * pom+ dGCVdR * pom& + dPOLdR1 * (erhead_tail(k,1)& -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))& - + dPOLdR2 * condor + dGLJdR * pom + + dPOLdR2 * condor + dGLJdR * pom+sgrad gvdwc(k,i) = gvdwc(k,i) & - dGCLdR * erhead(k)& @@ -26709,7 +27555,7 @@ chip1=chip(itypi) - dGCVdR * erhead(k)& - dPOLdR1 * erhead_tail(k,1)& - dPOLdR2 * erhead_tail(k,2)& - - dGLJdR * erhead(k) + - dGLJdR * erhead(k)-sgrad gvdwc(k,j) = gvdwc(k,j) & + dGCLdR * erhead(k) & @@ -26717,7 +27563,7 @@ chip1=chip(itypi) + dGCVdR * erhead(k) & + dPOLdR1 * erhead_tail(k,1) & + dPOLdR2 * erhead_tail(k,2)& - + dGLJdR * erhead(k) + + dGLJdR * erhead(k)+sgrad END DO RETURN @@ -26766,13 +27612,16 @@ chip1=chip(itypi) !c! Coulomb electrostatic interaction Ecl = (332.0d0 * Qij) / Rhead !c! derivative of Ecl is Gcl... - dGCLdR = (-332.0d0 * Qij ) / Rhead_sq + dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad + ECL=ECL*sss_ele_cut dGCLdOM1 = 0.0d0 dGCLdOM2 = 0.0d0 dGCLdOM12 = 0.0d0 + ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq)) Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0) debkap=debaykapcat(itypi,itypj) + if (energy_dec) write(iout,*) "egb",Qij,debkap,Fgb,a12sq,ee0 Egb = -(332.0d0 * Qij *& (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb ! print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out @@ -26782,7 +27631,8 @@ chip1=chip(itypi) -(332.0d0 * Qij *& (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb ) - dGGBdR = dGGBdFGB * dFGBdR + dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad + Egb=Egb*sss_ele_grad !c!------------------------------------------------------------------- !c! Fisocav - isotropic cavity creation term !c! or "how much energy it costs to put charged head in water" @@ -26803,7 +27653,9 @@ chip1=chip(itypi) !c! Derivative of Fisocav is GCV... dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2) dbot = 12.0d0 * al4 * pom ** 11.0d0 - dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig + dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut& + +FisoCav*sss_ele_grad + FisoCav=FisoCav*sss_ele_cut !c!------------------------------------------------------------------- !c! Epol !c! Polarization energy - charged heads polarize hydrophobic "neck" @@ -26830,13 +27682,14 @@ chip1=chip(itypi) * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 ) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))& * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 ) - dPOLdR1 = dPOLdFGB1 * dFGBdR1 + dPOLdR1 = dPOLdFGB1 * dFGBdR1!*sss_ele_cut+epol*sss_ele_grad !c! dPOLdR1 = 0.0d0 - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2!*sss_ele_cut+epol*sss_ele_grad !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 +! epol=epol*sss_ele_cut !c! dPOLdOM2 = 0.0d0 !c!------------------------------------------------------------------- !c! Elj @@ -26845,7 +27698,10 @@ chip1=chip(itypi) Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) !c! derivative of Elj is Glj dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))& - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut& + +(Elj+epol)*sss_ele_grad + Elj=Elj*sss_ele_cut + epol=epol*sss_ele_cut !c!------------------------------------------------------------------- !c! Return the results !c! These things do the dRdX derivatives, that is @@ -26922,7 +27778,7 @@ chip1=chip(itypi) double precision dcosom1(3),dcosom2(3) !c! used in Epol derivatives double precision facd3, facd4 - double precision federmaus, adler + double precision federmaus, adler,sgrad integer istate,ii,jj real (kind=8) :: Fgb ! print *,"CALLING EQUAD" @@ -26963,15 +27819,15 @@ chip1=chip(itypi) dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k)) gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k) !c! this acts on hydrophobic center of interaction - gvdwx(k,i)= gvdwx(k,i) - gg(k) & + gvdwx(k,i)= gvdwx(k,i) - gg(k)*sss_ele_cut & + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))& - + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv - gvdwx(k,j)= gvdwx(k,j) + gg(k) & + + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut + gvdwx(k,j)= gvdwx(k,j) + gg(k)*sss_ele_cut & + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))& - + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut !c! this acts on Calpha - gvdwc(k,i)=gvdwc(k,i)-gg(k) - gvdwc(k,j)=gvdwc(k,j)+gg(k) + gvdwc(k,i)=gvdwc(k,i)-gg(k)*sss_ele_cut + gvdwc(k,j)=gvdwc(k,j)+gg(k)*sss_ele_cut END DO !c! sc_grad is done, now we will compute eheadtail = 0.0d0 @@ -26989,16 +27845,40 @@ chip1=chip(itypi) jj = istate/ii d1 = dhead(1,ii,itypi,itypj) d2 = dhead(2,jj,itypi,itypj) - DO k = 1,3 - chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) - chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres) - Rhead_distance(k) = chead(k,2) - chead(k,1) - END DO + do k=1,3 + chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) + chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres) +! distance + enddo + call to_box (chead(1,1),chead(2,1),chead(3,1)) + call to_box (chead(1,2),chead(2,2),chead(3,2)) + +!c! head distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + + Rhead_distance(1)=boxshift(chead( 1, 2 ) - chead( 1,1 ),boxxsize) + Rhead_distance(2)=boxshift(chead( 2, 2 ) - chead( 2,1 ),boxysize) + Rhead_distance(3)=boxshift(chead( 3, 2 ) - chead( 3,1 ),boxzsize) +! 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))) + +! DO k = 1,3 +! chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) +! chead(k,2) = c(k, j+nres) + d2 * dc_norm(k, j+nres) +! Rhead_distance(k) = chead(k,2) - chead(k,1) +! END DO !c! 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 = dsqrt( & +! (Rhead_distance(1)*Rhead_distance(1)) & +! + (Rhead_distance(2)*Rhead_distance(2)) & +! + (Rhead_distance(3)*Rhead_distance(3))) END IF Rhead_sq = Rhead * Rhead @@ -27054,6 +27934,7 @@ chip1=chip(itypi) dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2) dbot = 12.0d0 * al4 * pom ** 11.0d0 dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig + !c! dGCVdR = 0.0d0 !c!------------------------------------------------------------------- !c! Polarization energy @@ -27160,6 +28041,7 @@ chip1=chip(itypi) pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) !c! this acts on hydrophobic center of interaction +! sgrad=sss_ele_grad*(Ecl+Egb+FisoCav+epol+Elj)*rij*rreal(k) gheadtail(k,1,1) = gheadtail(k,1,1) & - dGCLdR * pom & - dGGBdR * pom & @@ -27171,7 +28053,7 @@ chip1=chip(itypi) - dQUADdR * pom& - tuna(k) & + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))& - + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv + + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) !c! this acts on hydrophobic center of interaction @@ -27186,7 +28068,7 @@ chip1=chip(itypi) + dQUADdR * pom & + tuna(k) & + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & - + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut !c! this acts on Calpha gheadtail(k,3,1) = gheadtail(k,3,1) & @@ -27232,16 +28114,22 @@ chip1=chip(itypi) DO l = 1, 4 gheadtail(k,l,2) = gheadtail(k,l,2) / eheadtail END DO - gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2) - gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2) - gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2) - gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2) + gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)*sss_ele_cut + gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)*sss_ele_cut + gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)*sss_ele_cut + gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)*sss_ele_cut DO l = 1, 4 gheadtail(k,l,1) = 0.0d0 gheadtail(k,l,2) = 0.0d0 END DO END DO eheadtail = (-dlog(eheadtail)) / betaT + do k=1,3 + gvdwx(k,i) = gvdwx(k,i) - eheadtail*sss_ele_grad*rreal(k)*rij + gvdwx(k,j) = gvdwx(k,j) + eheadtail*sss_ele_grad*rreal(k)*rij + gvdwc(k,i) = gvdwc(k,i) - eheadtail*sss_ele_grad*rreal(k)*rij + gvdwc(k,j) = gvdwc(k,j) + eheadtail*sss_ele_grad*rreal(k)*rij + enddo dPOLdOM1 = 0.0d0 dPOLdOM2 = 0.0d0 dQUADdOM1 = 0.0d0 @@ -27285,7 +28173,8 @@ chip1=chip(itypi) dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & * (2.0d0 - 0.5d0 * ee1) ) & / (2.0d0 * fgb1) - dPOLdR1 = dPOLdFGB1 * dFGBdR1 + dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut +! epol=epol*sss_ele_cut !c! dPOLdR1 = 0.0d0 dPOLdOM1 = 0.0d0 dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 @@ -27302,13 +28191,16 @@ chip1=chip(itypi) facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) gvdwx(k,i) = gvdwx(k,i) & - - dPOLdR1 * hawk + - dPOLdR1 * hawk-epol*sss_ele_grad*rreal(k)*rij gvdwx(k,j) = gvdwx(k,j) & + dPOLdR1 * (erhead_tail(k,1) & - -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) + -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))& + +epol*sss_ele_grad*rreal(k)*rij - gvdwc(k,i) = gvdwc(k,i) - dPOLdR1 * erhead_tail(k,1) - gvdwc(k,j) = gvdwc(k,j) + dPOLdR1 * erhead_tail(k,1) + gvdwc(k,i) = gvdwc(k,i) - dPOLdR1 * erhead_tail(k,1)& + -epol*sss_ele_grad*rreal(k)*rij + gvdwc(k,j) = gvdwc(k,j) + dPOLdR1 * erhead_tail(k,1)& + +epol*sss_ele_grad*rreal(k)*rij END DO RETURN @@ -27346,7 +28238,8 @@ chip1=chip(itypi) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & * (2.0d0 - 0.5d0 * ee2) ) & / (2.0d0 * fgb2) - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut +! epol=epol*sss_ele_cut !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 @@ -27367,14 +28260,18 @@ chip1=chip(itypi) gvdwx(k,i) = gvdwx(k,i) & - dPOLdR2 * (erhead_tail(k,2) & - -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) + -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))& + -epol*sss_ele_grad*rreal(k)*rij gvdwx(k,j) = gvdwx(k,j) & - + dPOLdR2 * condor + + dPOLdR2 * condor+epol*sss_ele_grad*rreal(k)*rij + gvdwc(k,i) = gvdwc(k,i) & - - dPOLdR2 * erhead_tail(k,2) + - dPOLdR2 * erhead_tail(k,2)-epol*sss_ele_grad*rreal(k)*rij + gvdwc(k,j) = gvdwc(k,j) & - + dPOLdR2 * erhead_tail(k,2) + + dPOLdR2 * erhead_tail(k,2)+epol*sss_ele_grad*rreal(k)*rij + END DO RETURN @@ -27413,7 +28310,8 @@ chip1=chip(itypi) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & * (2.0d0 - 0.5d0 * ee2) ) & / (2.0d0 * fgb2) - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad + epol=epol*sss_ele_cut !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 @@ -27451,7 +28349,7 @@ chip1=chip(itypi) SUBROUTINE eqd(Ecl,Elj,Epol) use calc_data use comm_momo - double precision facd4, federmaus,ecl,elj,epol + double precision facd4, federmaus,ecl,elj,epol,sgrad alphapol1 = alphapol(itypi,itypj) w1 = wqdip(1,itypi,itypj) w2 = wqdip(2,itypi,itypj) @@ -27478,8 +28376,8 @@ chip1=chip(itypi) hawk = w2 * Qi * Qi * (1.0d0 - sqom2) Ecl = sparrow / Rhead**2.0d0 & - hawk / Rhead**4.0d0 - dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 & - + 4.0d0 * hawk / Rhead**5.0d0 + dGCLdR = (- 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut !c! dF/dom1 dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0) !c! dF/dom2 @@ -27503,7 +28401,7 @@ chip1=chip(itypi) dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & * (2.0d0 - 0.5d0 * ee1) ) & / (2.0d0 * fgb1) - dPOLdR1 = dPOLdFGB1 * dFGBdR1 + dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut !c! dPOLdR1 = 0.0d0 dPOLdOM1 = 0.0d0 dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 @@ -27515,7 +28413,7 @@ chip1=chip(itypi) !c! derivative of Elj is Glj dGLJdR = 4.0d0 * eps_head & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut DO k = 1, 3 erhead(k) = Rhead_distance(k)/Rhead erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1) @@ -27532,105 +28430,226 @@ chip1=chip(itypi) DO k = 1, 3 hawk = (erhead_tail(k,1) + & facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) - + sgrad=(epol+elj+ecl)*sss_ele_grad*rreal(k)*rij pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) gvdwx(k,i) = gvdwx(k,i) & - dGCLdR * pom& - dPOLdR1 * hawk & - - dGLJdR * pom - + - dGLJdR * pom & + -sgrad + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) gvdwx(k,j) = gvdwx(k,j) & + dGCLdR * pom & + dPOLdR1 * (erhead_tail(k,1) & -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) & - + dGLJdR * pom + + dGLJdR * pom+sgrad gvdwc(k,i) = gvdwc(k,i) & - dGCLdR * erhead(k) & - dPOLdR1 * erhead_tail(k,1) & - - dGLJdR * erhead(k) + - dGLJdR * erhead(k)-sgrad gvdwc(k,j) = gvdwc(k,j) & + dGCLdR * erhead(k) & + dPOLdR1 * erhead_tail(k,1) & - + dGLJdR * erhead(k) + + dGLJdR * erhead(k)+sgrad END DO RETURN END SUBROUTINE eqd - SUBROUTINE edq(Ecl,Elj,Epol) -! IMPLICIT NONE - use comm_momo - use calc_data - double precision facd3, adler,ecl,elj,epol - alphapol2 = alphapol(itypj,itypi) - w1 = wqdip(1,itypi,itypj) - w2 = wqdip(2,itypi,itypj) - pis = sig0head(itypi,itypj) - eps_head = epshead(itypi,itypj) + SUBROUTINE eqd_cat(Ecl,Elj,Epol) + use calc_data + use comm_momo + double precision facd4, federmaus,ecl,elj,epol + alphapol1 = alphapolcat(itypi,itypj) + w1 = wqdipcat(1,itypi,itypj) + w2 = wqdipcat(2,itypi,itypj) + pis = sig0headcat(itypi,itypj) + eps_head = epsheadcat(itypi,itypj) +! eps_head=0.0d0 +! w2=0.0d0 +! alphapol1=0.0d0 !c!------------------------------------------------------------------- -!c! R2 - distance between head of jth side chain and tail of ith sidechain - R2 = 0.0d0 +!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 - R2=R2+(chead(k,2)-ctail(k,1))**2 + R1=R1+(ctail(k,2)-chead(k,1))**2 END DO !c! Pitagoras - R2 = dsqrt(R2) + 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 * Qj * om1 - hawk = w2 * Qj * Qj * (1.0d0 - sqom2) - ECL = sparrow / Rhead**2.0d0 & + sparrow = w1 * Qi * om1 + hawk = w2 * Qi * Qi * (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 + dGCLdR =sss_ele_cut*(-2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0)+sss_ele_grad*ECL + ECL=ECL*sss_ele_cut !c! dF/dom1 - dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) + dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0) !c! dF/dom2 - dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0) + dGCLdOM2 = 0.0d0 ! + +!(2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0) + !c-------------------------------------------------------------------- !c Polarization energy !c Epol - MomoFac2 = (1.0d0 - chi2 * sqom1) - RR2 = R2 * R2 / MomoFac2 - ee2 = exp(-(RR2 / (4.0d0 * a12sq))) - fgb2 = sqrt(RR2 + a12sq * ee2) - epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 ) - dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) & - / (fgb2 ** 5.0d0) - dFGBdR2 = ( (R2 / MomoFac2) & - * ( 2.0d0 - (0.5d0 * ee2) ) ) & - / (2.0d0 * fgb2) - dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & - * (2.0d0 - 0.5d0 * ee2) ) & - / (2.0d0 * fgb2) - dPOLdR2 = dPOLdFGB2 * dFGBdR2 -!c! dPOLdR2 = 0.0d0 - dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 -!c! dPOLdOM1 = 0.0d0 + MomoFac1 = (1.0d0 - chi1 * sqom2) + RR1 = R1 * R1 / MomoFac1 + ee1 = exp(-( RR1 / (4.0d0 * a12sq) )) + fgb1 = sqrt( RR1 + a12sq * ee1) + epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0) +!c! epol = 0.0d0 +!c!------------------------------------------------------------------ +!c! 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 = 0.0d0 ! as om2 is 0 +! (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & +! * (2.0d0 - 0.5d0 * ee1) ) & +! / (2.0d0 * fgb1) + dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad +!c! dPOLdR1 = 0.0d0 + dPOLdOM1 = 0.0d0 +! dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 dPOLdOM2 = 0.0d0 + epol=epol*sss_ele_cut !c!------------------------------------------------------------------- !c! Elj pom = (pis / Rhead)**6.0d0 Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) !c! derivative of Elj is Glj - dGLJdR = 4.0d0 * eps_head & - * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + dGLJdR = 4.0d0 * eps_head*sss_ele_cut & + * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad + Elj=Elj*sss_ele_cut + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1) + END DO + + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) ) + facd1 = d1 * vbld_inv(i+nres) + + DO k = 1, 3 + hawk = (erhead_tail(k,1) + & + facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) + + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gradpepcatx(k,i) = gradpepcatx(k,i) & + - dGCLdR * pom& + - dPOLdR1 * hawk & + - dGLJdR * pom + +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepcatx(k,j) = gradpepcatx(k,j) & +! + dGCLdR * pom & +! + dPOLdR1 * (erhead_tail(k,1) & +! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) & +! + dGLJdR * pom + + + gradpepcat(k,i) = gradpepcat(k,i) & + - dGCLdR * erhead(k) & + - dPOLdR1 * erhead_tail(k,1) & + - dGLJdR * erhead(k) + + gradpepcat(k,j) = gradpepcat(k,j) & + + dGCLdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1) & + + dGLJdR * erhead(k) + + END DO + RETURN + END SUBROUTINE eqd_cat + + SUBROUTINE edq(Ecl,Elj,Epol) +! IMPLICIT NONE + use comm_momo + use calc_data + + double precision facd3, adler,ecl,elj,epol,sgrad + alphapol2 = alphapol(itypj,itypi) + w1 = wqdip(1,itypi,itypj) + w2 = wqdip(2,itypi,itypj) + pis = sig0head(itypi,itypj) + eps_head = epshead(itypi,itypj) +!c!------------------------------------------------------------------- +!c! R2 - distance between head of jth side chain and tail of ith sidechain + R2 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances + R2=R2+(chead(k,2)-ctail(k,1))**2 + END DO +!c! Pitagoras + R2 = dsqrt(R2) + +!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 * Qj * om1 + hawk = w2 * Qj * Qj * (1.0d0 - sqom2) + ECL = sparrow / Rhead**2.0d0 & + - hawk / Rhead**4.0d0 +!c!------------------------------------------------------------------- +!c! derivative of ecl is Gcl +!c! dF/dr part + dGCLdR =sss_ele_cut*(- 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0) +!c! dF/dom1 + dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0) +!c-------------------------------------------------------------------- +!c Polarization energy +!c Epol + MomoFac2 = (1.0d0 - chi2 * sqom1) + RR2 = R2 * R2 / MomoFac2 + ee2 = exp(-(RR2 / (4.0d0 * a12sq))) + fgb2 = sqrt(RR2 + a12sq * ee2) + epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 ) + dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) & + / (fgb2 ** 5.0d0) + dFGBdR2 = ( (R2 / MomoFac2) & + * ( 2.0d0 - (0.5d0 * ee2) ) ) & + / (2.0d0 * fgb2) + dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & + * (2.0d0 - 0.5d0 * ee2) ) & + / (2.0d0 * fgb2) + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut +!c! dPOLdR2 = 0.0d0 + dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 +!c! dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 +!c!------------------------------------------------------------------- +!c! Elj + pom = (pis / Rhead)**6.0d0 + Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) +!c! derivative of Elj is Glj + dGLJdR = 4.0d0 * eps_head & + * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut !c!------------------------------------------------------------------- !c! Return the results !c! (see comments in Eqq) @@ -27648,30 +28667,30 @@ chip1=chip(itypi) DO k = 1, 3 condor = (erhead_tail(k,2) & + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres))) - + sgrad=(epol+elj+ecl)*sss_ele_grad*rreal(k)*rij pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) gvdwx(k,i) = gvdwx(k,i) & - dGCLdR * pom & - dPOLdR2 * (erhead_tail(k,2) & -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) & - - dGLJdR * pom + - dGLJdR * pom-sgrad pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) gvdwx(k,j) = gvdwx(k,j) & + dGCLdR * pom & + dPOLdR2 * condor & - + dGLJdR * pom + + dGLJdR * pom+sgrad gvdwc(k,i) = gvdwc(k,i) & - dGCLdR * erhead(k) & - dPOLdR2 * erhead_tail(k,2) & - - dGLJdR * erhead(k) + - dGLJdR * erhead(k)-sgrad gvdwc(k,j) = gvdwc(k,j) & + dGCLdR * erhead(k) & + dPOLdR2 * erhead_tail(k,2) & - + dGLJdR * erhead(k) + + dGLJdR * erhead(k)+sgrad END DO RETURN @@ -27713,12 +28732,13 @@ chip1=chip(itypi) !c!------------------------------------------------------------------- !c! derivative of ecl is Gcl !c! dF/dr part - dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 & - + 4.0d0 * hawk / Rhead**5.0d0 + dGCLdR =( - 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut+ECL*sss_ele_grad !c! dF/dom1 dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) !c! dF/dom2 dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0) + ECL=ECL*sss_ele_cut !c-------------------------------------------------------------------- !c-------------------------------------------------------------------- !c Polarization energy @@ -27736,11 +28756,12 @@ chip1=chip(itypi) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & * (2.0d0 - 0.5d0 * ee2) ) & / (2.0d0 * fgb2) - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 dPOLdOM2 = 0.0d0 + epol=epol*sss_ele_cut !c!------------------------------------------------------------------- !c! Elj pom = (pis / Rhead)**6.0d0 @@ -27748,7 +28769,9 @@ chip1=chip(itypi) !c! derivative of Elj is Glj dGLJdR = 4.0d0 * eps_head & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+& + Elj*sss_ele_grad + Elj=Elj*sss_ele_cut !c!------------------------------------------------------------------- !c! Return the results @@ -27833,8 +28856,10 @@ chip1=chip(itypi) !c!------------------------------------------------------------------- !c! derivative of ecl is Gcl !c! dF/dr part - dGCLdR = - 2.0d0 * sparrow / Rhead**3.0d0 & - + 4.0d0 * hawk / Rhead**5.0d0 + dGCLdR = (- 2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut+& + ECL*sss_ele_grad + ECL=ECL*sss_ele_cut !c! dF/dom1 dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) !c! dF/dom2 @@ -27856,7 +28881,8 @@ chip1=chip(itypi) dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & * (2.0d0 - 0.5d0 * ee2) ) & / (2.0d0 * fgb2) - dPOLdR2 = dPOLdFGB2 * dFGBdR2 + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad + epol=epol*sss_ele_grad !c! dPOLdR2 = 0.0d0 dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 !c! dPOLdOM1 = 0.0d0 @@ -27866,9 +28892,10 @@ chip1=chip(itypi) pom = (pis / Rhead)**6.0d0 Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) !c! derivative of Elj is Glj - dGLJdR = 4.0d0 * eps_head & + dGLJdR = 4.0d0 * eps_head*sss_ele_cut & * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & - + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad + Elj=Elj*sss_ele_cut !c!------------------------------------------------------------------- !c! Return the results @@ -27955,7 +28982,7 @@ chip1=chip(itypi) c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0) c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) & * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2)) - dGCLdR = c1 - c2 + dGCLdR = (c1 - c2)*sss_ele_cut!+ECL*sss_ele_grad !c! dECL/dom1 c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0) c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & @@ -27983,15 +29010,141 @@ chip1=chip(itypi) DO k = 1, 3 pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) - gvdwx(k,i) = gvdwx(k,i) - dGCLdR * pom + gvdwx(k,i) = gvdwx(k,i)- dGCLdR * pom-(ecl*sss_ele_grad*Rreal(k)*rij) pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) - gvdwx(k,j) = gvdwx(k,j) + dGCLdR * pom + gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom+(ecl*sss_ele_grad*Rreal(k)*rij) - gvdwc(k,i) = gvdwc(k,i) - dGCLdR * erhead(k) - gvdwc(k,j) = gvdwc(k,j) + dGCLdR * erhead(k) + gvdwc(k,i) = gvdwc(k,i)- dGCLdR * erhead(k)-(ecl*sss_ele_grad*Rreal(k)*rij) + gvdwc(k,j) = gvdwc(k,j)+ dGCLdR * erhead(k)+(ecl*sss_ele_grad*Rreal(k)*rij) END DO RETURN END SUBROUTINE edd + SUBROUTINE edd_cat(ECL) +! IMPLICIT NONE + use comm_momo + use calc_data + + double precision ecl +!c! csig = sigiso(itypi,itypj) + w1 = wqdipcat(1,itypi,itypj) + w2 = wqdipcat(2,itypi,itypj) +! w2=0.0d0 +!c!------------------------------------------------------------------- +!c! ECL +! print *,"om1",om1,om2,om12 + fac = - 3.0d0 * om1 !after integer and simplify + c1 = (w1 / (Rhead**3.0d0)) * fac + c2 = (w2 / Rhead ** 6.0d0) & + * (4.0d0 + 6.0d0*sqom1 ) !after integration and simplification + ECL = c1 - c2 +!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 + 6.0d0*sqom1) + dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad +!c! dECL/dom1 + c1 = (-3.0d0 * w1) / (Rhead**3.0d0) + c2 = (12.0d0 * w2*om1) / (Rhead**6.0d0) + dGCLdOM1 = c1 - c2 +!c! dECL/dom2 +! c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0) + c1=0.0 ! this is because om2 is 0 +! c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & +! * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 ) + c2=0.0 !om is 0 + dGCLdOM2 = c1 - c2 +!c! dECL/dom12 +! c1 = w1 / (Rhead ** 3.0d0) + c1=0.0d0 ! this is because om12 is 0 +! c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + c2=0.0d0 !om12 is 0 + dGCLdOM12 = c1 - c2 +!c!------------------------------------------------------------------- +!c! Return the results +!c! (see comments in Eqq) + 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)) + gradpepcatx(k,i) = gradpepcatx(k,i) - dGCLdR * pom +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepcatx(k,j) = gradpepcatx(k,j) + dGCLdR * pom + + gradpepcat(k,i) = gradpepcat(k,i) - dGCLdR * erhead(k) + gradpepcat(k,j) = gradpepcat(k,j) + dGCLdR * erhead(k) + END DO + RETURN + END SUBROUTINE edd_cat + SUBROUTINE edd_cat_pep(ECL) +! IMPLICIT NONE + use comm_momo + use calc_data + + double precision ecl +!c! csig = sigiso(itypi,itypj) + w1 = wqdipcat(1,itypi,itypj) + w2 = wqdipcat(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)) + ECL = c1 - c2 +!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)) + dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad + ECL=ECL*sss_ele_cut +!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 ) + dGCLdOM1 = c1 - c2 +!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 ) + dGCLdOM2 = c1 - c2 + dGCLdOM2=0.0d0 ! this is because om2=0 +!c! dECL/dom12 + c1 = w1 / (Rhead ** 3.0d0) + c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + dGCLdOM12 = c1 - c2 + dGCLdOM12=0.0d0 !this is because om12=0.0 +!c!------------------------------------------------------------------- +!c! Return the results +!c! (see comments in Eqq) + DO k= 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + END DO + erdxi = scalar( erhead(1), dC_norm(1,i) ) + erdxj = scalar( erhead(1), dC_norm(1,j+nres) ) + facd1 = d1 * vbld_inv(i) + facd2 = d2 * vbld_inv(j+nres) + DO k = 1, 3 + + pom = facd1*(erhead(k)-erdxi*dC_norm(k,i)) + gradpepcat(k,i) = gradpepcat(k,i) + dGCLdR * pom + gradpepcat(k,i+1) = gradpepcat(k,i+1) - dGCLdR * pom +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepcatx(k,j) = gradpepcatx(k,j) + dGCLdR * pom + + gradpepcat(k,i) = gradpepcat(k,i) - dGCLdR * erhead(k)*0.5d0 + gradpepcat(k,i+1) = gradpepcat(k,i+1)- dGCLdR * erhead(k)*0.5d0 + gradpepcat(k,j) = gradpepcat(k,j) + dGCLdR * erhead(k) + END DO + RETURN + END SUBROUTINE edd_cat_pep + SUBROUTINE elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol) ! IMPLICIT NONE use comm_momo @@ -28379,11 +29532,238 @@ chip1=chip(itypi) gradtschebyshev=aux return end function gradtschebyshev +!!!!!!!!!-------------------------------------------------------------- + subroutine lipid_bond(elipbond) + real(kind=8) :: elipbond,fac,dist_sub,sumdist + real(kind=8), dimension(3):: dist + integer(kind=8) :: i,j,k,ibra,ityp,jtyp,ityp1 + elipbond=0.0d0 +! print *,"before",ilipbond_start,ilipbond_end + do i=ilipbond_start,ilipbond_end +! print *,i,i+1,"i,i+1" + ityp=itype(i,4) + ityp1=itype(i+1,4) +! print *,ityp,ityp1,"itype" + j=i+1 + if (ityp.eq.12) ibra=i + if ((ityp.eq.ntyp1_molec(4)).or.(ityp1.ge.ntyp1_molec(4)-1)) cycle + if (ityp.eq.(ntyp1_molec(4)-1)) then + !cofniecie do ostatnie GL1 +! i=ibra + j=ibra + else + j=i + endif + jtyp=itype(j,4) + do k=1,3 + dist(k)=c(k,j)-c(k,i+1) + enddo + sumdist=0.0d0 + do k=1,3 + sumdist=sumdist+dist(k)**2 + enddo + dist_sub=sqrt(sumdist) +! print *,"before",i,j,ityp1,ityp,jtyp + elipbond=elipbond+kbondlip*((dist_sub-lip_bond(jtyp,ityp1))**2) + fac=kbondlip*(dist_sub-lip_bond(jtyp,ityp1)) + do k=1,3 + gradlipbond(k,i+1)= gradlipbond(k,i+1)-fac*dist(k)/dist_sub + gradlipbond(k,j)=gradlipbond(k,j)+fac*dist(k)/dist_sub + enddo + if (energy_dec) write(iout,*) "lipbond",j,i+1,dist_sub,lip_bond(jtyp,ityp1),kbondlip,fac + enddo + elipbond=elipbond*0.5d0 + return + end subroutine lipid_bond +!--------------------------------------------------------------------------------------- + subroutine lipid_angle(elipang) + real(kind=8) :: elipang,alfa,xa(3),xb(3),alfaact,alfa0,force,fac,& + scalara,vnorm,wnorm,sss,sss_grad,eangle + integer :: i,j,k,l,m,ibra,ityp1,itypm1,itypp1 + elipang=0.0d0 +! print *,"ilipang_start,ilipang_end",ilipang_start,ilipang_end + do i=ilipang_start,ilipang_end +! do i=4,4 + +! the loop is centered on the central residue + itypm1=itype(i-1,4) + ityp1=itype(i,4) + itypp1=itype(i+1,4) +! print *,i,i,j,"processor",fg_rank + j=i-1 + k=i + l=i+1 + if (ityp1.eq.12) ibra=i + if ((itypm1.eq.ntyp1_molec(4)).or.(ityp1.eq.ntyp1_molec(4))& + .or.(itypp1.eq.ntyp1_molec(4))) cycle !cycle if any of the angles is dummy + if ((itypm1.eq.ntyp1_molec(4)-1).or.(itypp1.eq.ntyp1_molec(4)-1)) cycle + ! branching is only to one angle + if (ityp1.eq.ntyp1_molec(4)-1) then + k=ibra + j=ibra-1 + endif + itypm1=itype(j,4) + ityp1=itype(k,4) + do m=1,3 + xa(m)=c(m,j)-c(m,k) + xb(m)=c(m,l)-c(m,k) +! xb(m)=1.0d0 + enddo + vnorm=dsqrt(xa(1)*xa(1)+xa(2)*xa(2)+xa(3)*xa(3)) + wnorm=dsqrt(xb(1)*xb(1)+xb(2)*xb(2)+xb(3)*xb(3)) + scalara=(xa(1)*xb(1)+xa(2)*xb(2)+xa(3)*xb(3))/(vnorm*wnorm) +! if (((scalar*scalar).gt.0.99999999d0).and.(alfa0.eq.180.0d0)) cycle + + alfaact=scalara +! sss=sscale_martini_angle(alfaact) +! sss_grad=sscale_grad_martini_angle(alfaact) +! print *,sss_grad,"sss_grad",sss +! if (sss.le.0.0) cycle +! if (sss_grad.ne.0.0) print *,sss_grad,"sss_grad" + force=lip_angle_force(itypm1,ityp1,itypp1) + alfa0=lip_angle_angle(itypm1,ityp1,itypp1) + eangle=force*(alfaact-dcos(alfa0))*(alfaact-dcos(alfa0))*0.5d0 + elipang=elipang+eangle!*(1001.0d0-1000.0d0*sss) + fac=force*(alfaact-dcos(alfa0))!*(1001.0d0-1000.0d0*sss)-sss_grad*eangle*1000.0d0 + do m=1,3 + gradlipang(m,j)=gradlipang(m,j)+(fac &!/dsqrt(1.0d0-scalar*scalar)& + *(xb(m)-scalara*wnorm*xa(m)/vnorm)& + /(vnorm*wnorm))!-sss_grad*eangle*xa(m)/vnorm + + gradlipang(m,l)=gradlipang(m,l)+(fac & !/dsqrt(1.0d0-scalar*scalar)& + *(xa(m)-scalara*vnorm*xb(m)/wnorm)& + /(vnorm*wnorm))!+sss_grad*eangle*xb(m)/wnorm + + gradlipang(m,k)=gradlipang(m,k)-(fac)& !/dsqrt(1.0d0-scalar*scalar)& + *(xb(m)-scalara*wnorm*xa(m)/vnorm)& + /((vnorm*wnorm))-(fac & !/dsqrt(1.0d0-scalar*scalar)& + *(xa(m)-scalara*vnorm*xb(m)/wnorm)& + /(vnorm*wnorm))!-sss_grad*eangle*xa(m)/vnorm& + !-sss_grad*eangle*xb(m)/wnorm + + +! *(xb(m)*vnorm*wnorm)& +!-xa(m)*xa(m)*xb(m)*wnorm/vnorm)& + enddo + if (energy_dec) write(iout,*) "elipang",j,k,l,force,alfa0,alfaact,elipang + enddo + return + end subroutine lipid_angle +!-------------------------------------------------------------------- + subroutine lipid_lj(eliplj) + real(kind=8) :: eliplj,fac,sumdist,dist_sub,LJ1,LJ2,LJ,& + xj,yj,zj,xi,yi,zi,sss,sss_grad + real(kind=8), dimension(3):: dist + integer :: i,j,k,inum,ityp,jtyp + eliplj=0.0d0 + do inum=iliplj_start,iliplj_end + i=mlipljlisti(inum) + j=mlipljlistj(inum) +! print *,inum,i,j,"processor",fg_rank + ityp=itype(i,4) + jtyp=itype(j,4) + xi=c(1,i) + yi=c(2,i) + zi=c(3,i) + call to_box(xi,yi,zi) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + dist(1)=xj + dist(2)=yj + dist(3)=zj + ! do k=1,3 + ! dist(k)=c(k,j)-c(k,i) + ! enddo + sumdist=0.0d0 + do k=1,3 + sumdist=sumdist+dist(k)**2 + enddo + + dist_sub=sqrt(sumdist) + sss=sscale_martini(dist_sub) + if (energy_dec) write(iout,*) "LJ LIP bef",i,j,ityp,jtyp,dist_sub + if (sss.le.0.0) cycle + sss_grad=sscale_grad_martini(dist_sub) + LJ1 = (lip_sig(ityp,jtyp)/dist_sub)**6 + LJ2 = LJ1**2 + LJ = LJ2 - LJ1 + LJ = 4.0d0*lip_eps(ityp,jtyp)*LJ + eliplj = eliplj + LJ*sss + fac=4.0d0*lip_eps(ityp,jtyp)*(-6.0d0*LJ1/dist_sub+12.0d0*LJ2/dist_sub) + do k=1,3 + gradliplj(k,i)=gradliplj(k,i)+fac*dist(k)/dist_sub*sss-sss_grad*LJ*dist(k)/dist_sub + gradliplj(k,j)=gradliplj(k,j)-fac*dist(k)/dist_sub*sss+sss_grad*LJ*dist(k)/dist_sub + enddo + if (energy_dec) write(iout,'(a7,4i5,2f8.3)') "LJ LIP",i,j,ityp,jtyp,LJ,dist_sub + enddo + return + end subroutine lipid_lj +!-------------------------------------------------------------------------------------- + subroutine lipid_elec(elipelec) + real(kind=8) :: elipelec,fac,sumdist,dist_sub,xj,yj,zj,xi,yi,zi,EQ,& + sss,sss_grad + real(kind=8), dimension(3):: dist + integer :: i,j,k,inum,ityp,jtyp + elipelec=0.0d0 +! print *,"processor",fg_rank,ilip_elec_start,ilipelec_end + do inum=ilip_elec_start,ilipelec_end + i=mlipeleclisti(inum) + j=mlipeleclistj(inum) +! print *,inum,i,j,"processor",fg_rank + ityp=itype(i,4) + jtyp=itype(j,4) + xi=c(1,i) + yi=c(2,i) + zi=c(3,i) + call to_box(xi,yi,zi) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + dist(1)=xj + dist(2)=yj + dist(3)=zj +! do k=1,3 +! dist(k)=c(k,j)-c(k,i) +! enddo + sumdist=0.0d0 + do k=1,3 + sumdist=sumdist+dist(k)**2 + enddo + dist_sub=sqrt(sumdist) + sss=sscale_martini(dist_sub) +! print *,sss,dist_sub + if (energy_dec) write(iout,*) "EQ LIP",sss,dist_sub,i,j + if (sss.le.0.0) cycle + sss_grad=sscale_grad_martini(dist_sub) +! print *,"sss",sss,sss_grad + EQ=k_coulomb_lip*(ichargelipid(ityp)*ichargelipid(jtyp)/dist_sub) + elipelec=elipelec+EQ*sss + fac=k_coulomb_lip*(ichargelipid(ityp)*ichargelipid(jtyp)/sumdist)*sss + do k=1,3 + gradlipelec(k,i)=gradlipelec(k,i)+fac*dist(k)/dist_sub& + -sss_grad*EQ*dist(k)/dist_sub + gradlipelec(k,j)=gradlipelec(k,j)-fac*dist(k)/dist_sub& + +sss_grad*EQ*dist(k)/dist_sub + enddo + if (energy_dec) write(iout,*) "EQ LIP",i,j,ityp,jtyp,EQ,dist_sub,elipelec + enddo + return + end subroutine lipid_elec +!------------------------------------------------------------------------- subroutine make_SCSC_inter_list include 'mpif.h' - real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp - real*8 :: dist_init, dist_temp,r_buff_list + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: dist_init, dist_temp,r_buff_list integer:: contlisti(250*nres),contlistj(250*nres) ! integer :: newcontlisti(200*nres),newcontlistj(200*nres) integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_sc,g_ilist_sc @@ -28487,8 +29867,8 @@ chip1=chip(itypi) use MD_data, only: itime_mat include 'mpif.h' - real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp - real*8 :: dist_init, dist_temp,r_buff_list + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: dist_init, dist_temp,r_buff_list integer:: contlistscpi(350*nres),contlistscpj(350*nres) ! integer :: newcontlistscpi(200*nres),newcontlistscpj(200*nres) integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_scp,g_ilist_scp @@ -28613,10 +29993,10 @@ chip1=chip(itypi) subroutine make_pp_inter_list include 'mpif.h' - real*8 :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp - real*8 :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj - real*8 :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi - real*8 :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj + real(kind=8) :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi + real(kind=8) :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj integer:: contlistppi(250*nres),contlistppj(250*nres) ! integer :: newcontlistppi(200*nres),newcontlistppj(200*nres) integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_pp,g_ilist_pp @@ -28723,76 +30103,4457 @@ chip1=chip(itypi) #endif return end subroutine make_pp_inter_list +!--------------------------------------------------------------------------- + subroutine make_cat_pep_list + include 'mpif.h' + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj + real(kind=8) :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi + real(kind=8) :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj + real(kind=8) :: xja,yja,zja + integer:: contlistcatpnormi(300*nres),contlistcatpnormj(300*nres) + integer:: contlistcatscnormi(250*nres),contlistcatscnormj(250*nres) + integer:: contlistcatptrani(250*nres),contlistcatptranj(250*nres) + integer:: contlistcatsctrani(250*nres),contlistcatsctranj(250*nres) + integer:: contlistcatscangi(250*nres),contlistcatscangj(250*nres) + integer:: contlistcatscangfi(250*nres),contlistcatscangfj(250*nres),& + contlistcatscangfk(250*nres) + integer:: contlistcatscangti(250*nres),contlistcatscangtj(250*nres) + integer:: contlistcatscangtk(250*nres),contlistcatscangtl(250*nres) -!----------------------------------------------------------------------------- - double precision function boxshift(x,boxsize) - implicit none - double precision x,boxsize - double precision xtemp - xtemp=dmod(x,boxsize) - if (dabs(xtemp-boxsize).lt.dabs(xtemp)) then - boxshift=xtemp-boxsize - else if (dabs(xtemp+boxsize).lt.dabs(xtemp)) then - boxshift=xtemp+boxsize - else - boxshift=xtemp - endif - return - end function boxshift -!----------------------------------------------------------------------------- - subroutine to_box(xi,yi,zi) - implicit none -! include 'DIMENSIONS' -! include 'COMMON.CHAIN' - double precision xi,yi,zi - xi=dmod(xi,boxxsize) - if (xi.lt.0.0d0) xi=xi+boxxsize - yi=dmod(yi,boxysize) - if (yi.lt.0.0d0) yi=yi+boxysize - zi=dmod(zi,boxzsize) - if (zi.lt.0.0d0) zi=zi+boxzsize - return - end subroutine to_box -!-------------------------------------------------------------------------- - subroutine lipid_layer(xi,yi,zi,sslipi,ssgradlipi) - implicit none -! include 'DIMENSIONS' -! include 'COMMON.IOUNITS' -! include 'COMMON.CHAIN' - double precision xi,yi,zi,sslipi,ssgradlipi - double precision fracinbuf -! double precision sscalelip,sscagradlip + +! integer :: newcontlistppi(200*nres),newcontlistppj(200*nres) + integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_catscnorm,& + ilist_catsctran,ilist_catpnorm,ilist_catptran,itmp,ilist_catscang,& + ilist_catscangf,ilist_catscangt,k + integer displ(0:nprocs),i_ilist_catscnorm(0:nprocs),ierr,& + i_ilist_catpnorm(0:nprocs),i_ilist_catsctran(0:nprocs),& + i_ilist_catptran(0:nprocs),i_ilist_catscang(0:nprocs),& + i_ilist_catscangf(0:nprocs),i_ilist_catscangt(0:nprocs) +! write(iout,*),"START make_pp",iatel_s,iatel_e,r_cut_ele+r_buff_list + ilist_catpnorm=0 + ilist_catscnorm=0 + ilist_catptran=0 + ilist_catsctran=0 + ilist_catscang=0 + + + r_buff_list=6.0 + itmp=0 + do i=1,4 + itmp=itmp+nres_molec(i) + enddo +! go to 17 +! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization + do i=ibond_start,ibond_end + +! print *,"I am in EVDW",i + itypi=iabs(itype(i,1)) + +! if (i.ne.47) cycle + if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle +! itypi1=iabs(itype(i+1,1)) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + call to_box(xi,yi,zi) + dxi=dc_norm(1,i) + dyi=dc_norm(2,i) + dzi=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 + call to_box(xmedi,ymedi,zmedi) + +! dsci_inv=vbld_inv(i+nres) + do j=itmp+1,itmp+nres_molec(5) + dxj=dc(1,j) + dyj=dc(2,j) + dzj=dc(3,j) + dx_normj=dc_norm(1,j) + dy_normj=dc_norm(2,j) + dz_normj=dc_norm(3,j) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) +! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) +! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0 + xja=boxshift(xj-xmedi,boxxsize) + yja=boxshift(yj-ymedi,boxysize) + zja=boxshift(zj-zmedi,boxzsize) + dist_init=xja**2+yja**2+zja**2 + if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then +! Here the list is created + if (itype(j,5).le.5) then + ilist_catpnorm=ilist_catpnorm+1 +! this can be substituted by cantor and anti-cantor + contlistcatpnormi(ilist_catpnorm)=i + contlistcatpnormj(ilist_catpnorm)=j + else + ilist_catptran=ilist_catptran+1 +! this can be substituted by cantor and anti-cantor + contlistcatptrani(ilist_catptran)=i + contlistcatptranj(ilist_catptran)=j + endif + endif + xja=boxshift(xj-xi,boxxsize) + yja=boxshift(yj-yi,boxysize) + zja=boxshift(zj-zi,boxzsize) + dist_init=xja**2+yja**2+zja**2 + if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then +! Here the list is created + if (itype(j,5).le.5) then + ilist_catscnorm=ilist_catscnorm+1 +! this can be substituted by cantor and anti-cantor +! write(iout,*) "have contact",i,j,ilist_catscnorm + contlistcatscnormi(ilist_catscnorm)=i + contlistcatscnormj(ilist_catscnorm)=j +! write(iout,*) "have contact2",i,j,ilist_catscnorm,& +! contlistcatscnormi(ilist_catscnorm),contlistcatscnormj(ilist_catscnorm) + + else + ilist_catsctran=ilist_catsctran+1 +! this can be substituted by cantor and anti-cantor + contlistcatsctrani(ilist_catsctran)=i + contlistcatsctranj(ilist_catsctran)=j +! print *,"KUR**",i,j,itype(i,1) + if (((itype(i,1).eq.1).or.(itype(i,1).eq.15).or.& + (itype(i,1).eq.16).or.(itype(i,1).eq.17)).and.& + ((sqrt(dist_init).le.(r_cut_ang+r_buff_list)))) then +! print *,"KUR**2",i,j,itype(i,1),ilist_catscang+1 + + ilist_catscang=ilist_catscang+1 + contlistcatscangi(ilist_catscang)=i + contlistcatscangj(ilist_catscang)=j + endif + + endif + endif +! enddo + enddo + enddo #ifdef DEBUG - write (iout,*) "bordlipbot",bordlipbot," bordliptop",bordliptop - write (iout,*) "buflipbot",buflipbot," lipbufthick",lipbufthick - write (iout,*) "xi yi zi",xi,yi,zi + write (iout,*) "before MPIREDUCE",ilist_catsctran,ilist_catptran,& + ilist_catscnorm,ilist_catpnorm,ilist_catscang + + do i=1,ilist_catsctran + write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i),& + itype(j,contlistcatsctranj(i)) + enddo + do i=1,ilist_catptran + write (iout,*) i,contlistcatptrani(i),contlistcatsctranj(i) + enddo + do i=1,ilist_catscnorm + write (iout,*) i,contlistcatscnormi(i),contlistcatscnormj(i) + enddo + do i=1,ilist_catpnorm + write (iout,*) i,contlistcatpnormi(i),contlistcatscnormj(i) + enddo + do i=1,ilist_catscang + write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i) + enddo + + #endif - if ((zi.gt.bordlipbot).and.(zi.lt.bordliptop)) then -! the energy transfer exist - if (zi.lt.buflipbot) then -! what fraction I am in - fracinbuf=1.0d0-((zi-bordlipbot)/lipbufthick) -! lipbufthick is thickenes of lipid buffore - sslipi=sscalelip(fracinbuf) - ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick - elseif (zi.gt.bufliptop) then - fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) - sslipi=sscalelip(fracinbuf) - ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + if (nfgtasks.gt.1)then + + call MPI_Reduce(ilist_catsctran,g_ilist_catsctran,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catsctran,1,MPI_INTEGER,& + i_ilist_catsctran,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catsctran(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatsctrani,ilist_catsctran,MPI_INTEGER,& + newcontlistcatsctrani,i_ilist_catsctran,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatsctranj,ilist_catsctran,MPI_INTEGER,& + newcontlistcatsctranj,i_ilist_catsctran,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catsctran,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatsctrani,g_ilist_catsctran,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatsctranj,g_ilist_catsctran,MPI_INT,king,FG_COMM,IERR) + + + call MPI_Reduce(ilist_catptran,g_ilist_catptran,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catptran,1,MPI_INTEGER,& + i_ilist_catptran,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catptran(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatptrani,ilist_catptran,MPI_INTEGER,& + newcontlistcatptrani,i_ilist_catptran,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatptranj,ilist_catptran,MPI_INTEGER,& + newcontlistcatptranj,i_ilist_catptran,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catptran,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatptrani,g_ilist_catptran,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatptranj,g_ilist_catptran,MPI_INT,king,FG_COMM,IERR) + +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + + call MPI_Reduce(ilist_catscnorm,g_ilist_catscnorm,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catscnorm,1,MPI_INTEGER,& + i_ilist_catscnorm,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catscnorm(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatscnormi,ilist_catscnorm,MPI_INTEGER,& + newcontlistcatscnormi,i_ilist_catscnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscnormj,ilist_catscnorm,MPI_INTEGER,& + newcontlistcatscnormj,i_ilist_catscnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catscnorm,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatscnormi,g_ilist_catscnorm,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscnormj,g_ilist_catscnorm,MPI_INT,king,FG_COMM,IERR) + + + + call MPI_Reduce(ilist_catpnorm,g_ilist_catpnorm,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catpnorm,1,MPI_INTEGER,& + i_ilist_catpnorm,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catpnorm(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatpnormi,ilist_catpnorm,MPI_INTEGER,& + newcontlistcatpnormi,i_ilist_catpnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatpnormj,ilist_catpnorm,MPI_INTEGER,& + newcontlistcatpnormj,i_ilist_catpnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catpnorm,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatpnormi,g_ilist_catpnorm,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatpnormj,g_ilist_catpnorm,MPI_INT,king,FG_COMM,IERR) + + + + call MPI_Reduce(ilist_catscang,g_ilist_catscang,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catscang,1,MPI_INTEGER,& + i_ilist_catscang,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catscang(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatscangi,ilist_catscang,MPI_INTEGER,& + newcontlistcatscangi,i_ilist_catscang,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangj,ilist_catscang,MPI_INTEGER,& + newcontlistcatscangj,i_ilist_catscang,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catscang,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatscangi,g_ilist_catscang,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangj,g_ilist_catscang,MPI_INT,king,FG_COMM,IERR) + + else - sslipi=1.0d0 - ssgradlipi=0.0 + g_ilist_catscnorm=ilist_catscnorm + g_ilist_catsctran=ilist_catsctran + g_ilist_catpnorm=ilist_catpnorm + g_ilist_catptran=ilist_catptran + g_ilist_catscang=ilist_catscang + + + do i=1,ilist_catscnorm + newcontlistcatscnormi(i)=contlistcatscnormi(i) + newcontlistcatscnormj(i)=contlistcatscnormj(i) + enddo + do i=1,ilist_catpnorm + newcontlistcatpnormi(i)=contlistcatpnormi(i) + newcontlistcatpnormj(i)=contlistcatpnormj(i) + enddo + do i=1,ilist_catsctran + newcontlistcatsctrani(i)=contlistcatsctrani(i) + newcontlistcatsctranj(i)=contlistcatsctranj(i) + enddo + do i=1,ilist_catptran + newcontlistcatptrani(i)=contlistcatptrani(i) + newcontlistcatptranj(i)=contlistcatptranj(i) + enddo + + do i=1,ilist_catscang + newcontlistcatscangi(i)=contlistcatscangi(i) + newcontlistcatscangj(i)=contlistcatscangj(i) + enddo + + endif - else - sslipi=0.0d0 - ssgradlipi=0.0 - endif + call int_bounds(g_ilist_catsctran,g_listcatsctran_start,g_listcatsctran_end) + call int_bounds(g_ilist_catptran,g_listcatptran_start,g_listcatptran_end) + call int_bounds(g_ilist_catscnorm,g_listcatscnorm_start,g_listcatscnorm_end) + call int_bounds(g_ilist_catpnorm,g_listcatpnorm_start,g_listcatpnorm_end) + call int_bounds(g_ilist_catscang,g_listcatscang_start,g_listcatscang_end) +! make new ang list + ilist_catscangf=0 + do i=g_listcatscang_start,g_listcatscang_end + do j=2,g_ilist_catscang +! print *,"RWA",i,j,contlistcatscangj(i),contlistcatscangj(j) + if (j.le.i) cycle + if (newcontlistcatscangj(i).ne.newcontlistcatscangj(j)) cycle + ilist_catscangf=ilist_catscangf+1 + contlistcatscangfi(ilist_catscangf)=newcontlistcatscangi(i) + contlistcatscangfj(ilist_catscangf)=newcontlistcatscangj(i) + contlistcatscangfk(ilist_catscangf)=newcontlistcatscangi(j) +! print *,"TUTU",g_listcatscang_start,g_listcatscang_end,i,j,g_ilist_catscangf,myrank + enddo + enddo + if (nfgtasks.gt.1)then + + call MPI_Reduce(ilist_catscangf,g_ilist_catscangf,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catscangf,1,MPI_INTEGER,& + i_ilist_catscangf,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catscangf(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatscangfi,ilist_catscangf,MPI_INTEGER,& + newcontlistcatscangfi,i_ilist_catscangf,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangfj,ilist_catscangf,MPI_INTEGER,& + newcontlistcatscangfj,i_ilist_catscangf,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangfk,ilist_catscangf,MPI_INTEGER,& + newcontlistcatscangfk,i_ilist_catscangf,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + + call MPI_Bcast(g_ilist_catscangf,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatscangfi,g_ilist_catscangf,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangfj,g_ilist_catscangf,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangfk,g_ilist_catscangf,MPI_INT,king,FG_COMM,IERR) + else + g_ilist_catscangf=ilist_catscangf + do i=1,ilist_catscangf + newcontlistcatscangfi(i)=contlistcatscangfi(i) + newcontlistcatscangfj(i)=contlistcatscangfj(i) + newcontlistcatscangfk(i)=contlistcatscangfk(i) + enddo + endif + call int_bounds(g_ilist_catscangf,g_listcatscangf_start,g_listcatscangf_end) + + + ilist_catscangt=0 + do i=g_listcatscang_start,g_listcatscang_end + do j=1,g_ilist_catscang + do k=1,g_ilist_catscang +! print *,"TUTU1",g_listcatscang_start,g_listcatscang_end,i,j + + if (newcontlistcatscangj(i).ne.newcontlistcatscangj(j)) cycle + if (newcontlistcatscangj(i).ne.newcontlistcatscangj(k)) cycle + if (newcontlistcatscangj(k).ne.newcontlistcatscangj(j)) cycle + if (newcontlistcatscangi(i).eq.newcontlistcatscangi(j)) cycle + if (newcontlistcatscangi(i).eq.newcontlistcatscangi(k)) cycle + if (newcontlistcatscangi(k).eq.newcontlistcatscangi(j)) cycle +! print *,"TUTU2",g_listcatscang_start,g_listcatscang_end,i,j + + ilist_catscangt=ilist_catscangt+1 + contlistcatscangti(ilist_catscangt)=newcontlistcatscangi(i) + contlistcatscangtj(ilist_catscangt)=newcontlistcatscangj(i) + contlistcatscangtk(ilist_catscangt)=newcontlistcatscangi(j) + contlistcatscangtl(ilist_catscangt)=newcontlistcatscangi(k) + + enddo + enddo + enddo + if (nfgtasks.gt.1)then + + call MPI_Reduce(ilist_catscangt,g_ilist_catscangt,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catscangt,1,MPI_INTEGER,& + i_ilist_catscangt,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catscangt(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatscangti,ilist_catscangt,MPI_INTEGER,& + newcontlistcatscangti,i_ilist_catscangt,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangtj,ilist_catscangt,MPI_INTEGER,& + newcontlistcatscangtj,i_ilist_catscangt,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangtk,ilist_catscangt,MPI_INTEGER,& + newcontlistcatscangtk,i_ilist_catscangt,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatscangtl,ilist_catscangt,MPI_INTEGER,& + newcontlistcatscangtl,i_ilist_catscangt,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + + call MPI_Bcast(g_ilist_catscangt,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatscangti,g_ilist_catscangt,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangtj,g_ilist_catscangt,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangtk,g_ilist_catscangt,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatscangtl,g_ilist_catscangt,MPI_INT,king,FG_COMM,IERR) + + else + g_ilist_catscangt=ilist_catscangt + do i=1,ilist_catscangt + newcontlistcatscangti(i)=contlistcatscangti(i) + newcontlistcatscangtj(i)=contlistcatscangtj(i) + newcontlistcatscangtk(i)=contlistcatscangtk(i) + newcontlistcatscangtl(i)=contlistcatscangtl(i) + enddo + endif + call int_bounds(g_ilist_catscangt,g_listcatscangt_start,g_listcatscangt_end) + + + + + #ifdef DEBUG - write (iout,*) "sslipi",sslipi," ssgradlipi",ssgradlipi + write (iout,*) "after MPIREDUCE",ilist_catsctran,ilist_catptran, & + ilist_catscnorm,ilist_catpnorm + + do i=1,g_ilist_catsctran + write (iout,*) i,newcontlistcatsctrani(i),newcontlistcatsctranj(i) + enddo + do i=1,g_ilist_catptran + write (iout,*) i,newcontlistcatptrani(i),newcontlistcatsctranj(i) + enddo + do i=1,g_ilist_catscnorm + write (iout,*) i,newcontlistcatscnormi(i),newcontlistcatscnormj(i) + enddo + do i=1,g_ilist_catpnorm + write (iout,*) i,newcontlistcatpnormi(i),newcontlistcatscnormj(i) + enddo + do i=1,g_ilist_catscang + write (iout,*) i,newcontlistcatscangi(i),newcontlistcatscangj(i) + enddo #endif return - end subroutine lipid_layer + end subroutine make_cat_pep_list -!-------------------------------------------------------------------------- -!-------------------------------------------------------------------------- + subroutine make_lip_pep_list + include 'mpif.h' + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj + real(kind=8) :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi + real(kind=8) :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj + real(kind=8) :: xja,yja,zja + integer:: contlistmartpi(300*nres),contlistmartpj(300*nres) + integer:: contlistmartsci(250*nres),contlistmartscj(250*nres) + + +! integer :: newcontlistppi(200*nres),newcontlistppj(200*nres) + integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_martsc,& + ilist_martp,k,itmp + integer displ(0:nprocs),i_ilist_martsc(0:nprocs),ierr,& + i_ilist_martp(0:nprocs) +! write(iout,*),"START make_pp",iatel_s,iatel_e,r_cut_ele+r_buff_list + ilist_martp=0 + ilist_martsc=0 + + + r_buff_list=6.0 + itmp=0 + do i=1,3 + itmp=itmp+nres_molec(i) + enddo +! go to 17 +! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization + do i=ibond_start,ibond_end + +! print *,"I am in EVDW",i + itypi=iabs(itype(i,1)) + +! if (i.ne.47) cycle + if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle +! itypi1=iabs(itype(i+1,1)) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + call to_box(xi,yi,zi) + dxi=dc_norm(1,i) + dyi=dc_norm(2,i) + dzi=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 + call to_box(xmedi,ymedi,zmedi) + +! dsci_inv=vbld_inv(i+nres) + do j=itmp+1,itmp+nres_molec(4) + dxj=dc(1,j) + dyj=dc(2,j) + dzj=dc(3,j) + dx_normj=dc_norm(1,j) + dy_normj=dc_norm(2,j) + dz_normj=dc_norm(3,j) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) +! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) +! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0 + xja=boxshift(xj-xmedi,boxxsize) + yja=boxshift(yj-ymedi,boxysize) + zja=boxshift(zj-zmedi,boxzsize) + dist_init=xja**2+yja**2+zja**2 + if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then +! Here the list is created + ilist_martp=ilist_martp+1 +! this can be substituted by cantor and anti-cantor + contlistmartpi(ilist_martp)=i + contlistmartpj(ilist_martp)=j + endif + xja=boxshift(xj-xi,boxxsize) + yja=boxshift(yj-yi,boxysize) + zja=boxshift(zj-zi,boxzsize) + dist_init=xja**2+yja**2+zja**2 + if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then +! Here the list is created + ilist_martsc=ilist_martsc+1 +! this can be substituted by cantor and anti-cantor +! write(iout,*) "have contact",i,j,ilist_martsc + contlistmartsci(ilist_martsc)=i + contlistmartscj(ilist_martsc)=j +! write(iout,*) "have contact2",i,j,ilist_martsc,& +! contlistmartsci(ilist_martsc),contlistmartscj(ilist_martsc) + endif +! enddo + enddo + enddo +#ifdef DEBUG + write (iout,*) "before MPIREDUCE",ilist_catsctran,ilist_catptran,& + ilist_catscnorm,ilist_catpnorm,ilist_catscang + + do i=1,ilist_catsctran + write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i),& + itype(j,contlistcatsctranj(i)) + enddo + do i=1,ilist_catptran + write (iout,*) i,contlistcatptrani(i),contlistcatsctranj(i) + enddo + do i=1,ilist_catscnorm + write (iout,*) i,contlistcatscnormi(i),contlistcatscnormj(i) + enddo + do i=1,ilist_catpnorm + write (iout,*) i,contlistcatpnormi(i),contlistcatscnormj(i) + enddo + do i=1,ilist_catscang + write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i) + enddo + + +#endif + if (nfgtasks.gt.1)then + +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + + call MPI_Reduce(ilist_martsc,g_ilist_martsc,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_martsc,1,MPI_INTEGER,& + i_ilist_martsc,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_martsc(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistmartsci,ilist_martsc,MPI_INTEGER,& + newcontlistmartsci,i_ilist_martsc,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistmartscj,ilist_martsc,MPI_INTEGER,& + newcontlistmartscj,i_ilist_martsc,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_martsc,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistmartsci,g_ilist_martsc,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistmartscj,g_ilist_martsc,MPI_INT,king,FG_COMM,IERR) + + + + call MPI_Reduce(ilist_martp,g_ilist_martp,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_martp,1,MPI_INTEGER,& + i_ilist_martp,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_martp(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistmartpi,ilist_martp,MPI_INTEGER,& + newcontlistmartpi,i_ilist_martp,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistmartpj,ilist_martp,MPI_INTEGER,& + newcontlistmartpj,i_ilist_martp,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_martp,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistmartpi,g_ilist_martp,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistmartpj,g_ilist_martp,MPI_INT,king,FG_COMM,IERR) + + + + else + g_ilist_martsc=ilist_martsc + g_ilist_martp=ilist_martp + + + do i=1,ilist_martsc + newcontlistmartsci(i)=contlistmartsci(i) + newcontlistmartscj(i)=contlistmartscj(i) + enddo + do i=1,ilist_martp + newcontlistmartpi(i)=contlistmartpi(i) + newcontlistmartpj(i)=contlistmartpj(i) + enddo + endif + call int_bounds(g_ilist_martsc,g_listmartsc_start,g_listmartsc_end) + call int_bounds(g_ilist_martp,g_listmartp_start,g_listmartp_end) +! print *,"TUTU",g_listcatscang_start,g_listcatscang_end,i,j,g_ilist_catscangf,myrank + +#ifdef DEBUG + write (iout,*) "after MPIREDUCE",ilist_catsctran,ilist_catptran, & + ilist_catscnorm,ilist_catpnorm + + do i=1,g_ilist_catsctran + write (iout,*) i,newcontlistcatsctrani(i),newcontlistcatsctranj(i) + enddo + do i=1,g_ilist_catptran + write (iout,*) i,newcontlistcatptrani(i),newcontlistcatsctranj(i) + enddo + do i=1,g_ilist_catscnorm + write (iout,*) i,newcontlistcatscnormi(i),newcontlistcatscnormj(i) + enddo + do i=1,g_ilist_catpnorm + write (iout,*) i,newcontlistcatpnormi(i),newcontlistcatscnormj(i) + enddo + do i=1,g_ilist_catscang + write (iout,*) i,newcontlistcatscangi(i),newcontlistcatscangj(i) +#endif + return + end subroutine make_lip_pep_list + + + subroutine make_cat_cat_list + include 'mpif.h' + real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp + real(kind=8) :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj + real(kind=8) :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi + real(kind=8) :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj + real(kind=8) :: xja,yja,zja + integer,dimension(:),allocatable:: contlistcatpnormi,contlistcatpnormj +! integer :: newcontlistppi(200*nres),newcontlistppj(200*nres) + integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_catscnorm,& + ilist_catsctran,ilist_catpnorm,ilist_catptran,itmp,ilist_catscang,& + ilist_catscangf,ilist_catscangt,k + integer displ(0:nprocs),i_ilist_catscnorm(0:nprocs),ierr,& + i_ilist_catpnorm(0:nprocs),i_ilist_catsctran(0:nprocs),& + i_ilist_catptran(0:nprocs),i_ilist_catscang(0:nprocs),& + i_ilist_catscangf(0:nprocs),i_ilist_catscangt(0:nprocs) +! write(iout,*),"START make_catcat" + ilist_catpnorm=0 + ilist_catscnorm=0 + ilist_catptran=0 + ilist_catsctran=0 + ilist_catscang=0 + + if (.not.allocated(contlistcatpnormi)) then + allocate(contlistcatpnormi(900*nres)) + allocate(contlistcatpnormj(900*nres)) + endif + r_buff_list=3.0 + itmp=0 + do i=1,4 + itmp=itmp+nres_molec(i) + enddo +! go to 17 +! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization + do i=icatb_start,icatb_end + xi=c(1,i) + yi=c(2,i) + zi=c(3,i) + call to_box(xi,yi,zi) + dxi=dc_norm(1,i) + dyi=dc_norm(2,i) + dzi=dc_norm(3,i) +! dsci_inv=vbld_inv(i+nres) + do j=i+1,itmp+nres_molec(5) + dxj=dc(1,j) + dyj=dc(2,j) + dzj=dc(3,j) + dx_normj=dc_norm(1,j) + dy_normj=dc_norm(2,j) + dz_normj=dc_norm(3,j) + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) +! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) +! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0 + xja=boxshift(xj-xi,boxxsize) + yja=boxshift(yj-yi,boxysize) + zja=boxshift(zj-zi,boxzsize) + dist_init=xja**2+yja**2+zja**2 + if (sqrt(dist_init).le.(10.0+r_buff_list)) then +! Here the list is created +! if (i.eq.2) then +! print *,i,j,dist_init,ilist_catpnorm +! endif + ilist_catpnorm=ilist_catpnorm+1 + +! this can be substituted by cantor and anti-cantor + contlistcatpnormi(ilist_catpnorm)=i + contlistcatpnormj(ilist_catpnorm)=j + endif +! enddo + enddo + enddo +#ifdef DEBUG + write (iout,*) "before MPIREDUCE",ilist_catsctran,ilist_catptran,& + ilist_catscnorm,ilist_catpnorm,ilist_catscang + + do i=1,ilist_catpnorm + write (iout,*) i,contlistcatpnormi(i) + enddo + + +#endif + if (nfgtasks.gt.1)then + + call MPI_Reduce(ilist_catpnorm,g_ilist_catcatnorm,1,& + MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc + call MPI_Gather(ilist_catpnorm,1,MPI_INTEGER,& + i_ilist_catpnorm,1,MPI_INTEGER,king,FG_COMM,IERR) + displ(0)=0 + do i=1,nfgtasks-1,1 + displ(i)=i_ilist_catpnorm(i-1)+displ(i-1) + enddo +! write(iout,*) "before gather",displ(0),displ(1) + call MPI_Gatherv(contlistcatpnormi,ilist_catpnorm,MPI_INTEGER,& + newcontlistcatcatnormi,i_ilist_catpnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Gatherv(contlistcatpnormj,ilist_catpnorm,MPI_INTEGER,& + newcontlistcatcatnormj,i_ilist_catpnorm,displ,MPI_INTEGER,& + king,FG_COMM,IERR) + call MPI_Bcast(g_ilist_catcatnorm,1,MPI_INT,king,FG_COMM,IERR) +! write(iout,*) "before bcast",g_ilist_sc +! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM) + call MPI_Bcast(newcontlistcatcatnormi,g_ilist_catcatnorm,MPI_INT,king,FG_COMM,IERR) + call MPI_Bcast(newcontlistcatcatnormj,g_ilist_catcatnorm,MPI_INT,king,FG_COMM,IERR) + + + else + g_ilist_catcatnorm=ilist_catpnorm + do i=1,ilist_catpnorm + newcontlistcatcatnormi(i)=contlistcatpnormi(i) + newcontlistcatcatnormj(i)=contlistcatpnormj(i) + enddo + endif + call int_bounds(g_ilist_catcatnorm,g_listcatcatnorm_start,g_listcatcatnorm_end) + +#ifdef DEBUG + write (iout,*) "after MPIREDUCE",g_ilist_catcatnorm + + do i=1,g_ilist_catcatnorm + write (iout,*) i,newcontlistcatcatnormi(i),newcontlistcatcatnormj(i) + enddo +#endif +! write(iout,*),"END make_catcat" + return + end subroutine make_cat_cat_list + + +!----------------------------------------------------------------------------- + double precision function boxshift(x,boxsize) + implicit none + double precision x,boxsize + double precision xtemp + xtemp=dmod(x,boxsize) + if (dabs(xtemp-boxsize).lt.dabs(xtemp)) then + boxshift=xtemp-boxsize + else if (dabs(xtemp+boxsize).lt.dabs(xtemp)) then + boxshift=xtemp+boxsize + else + boxshift=xtemp + endif + return + end function boxshift +!----------------------------------------------------------------------------- + subroutine to_box(xi,yi,zi) + implicit none +! include 'DIMENSIONS' +! include 'COMMON.CHAIN' + double precision xi,yi,zi + xi=dmod(xi,boxxsize) + if (xi.lt.0.0d0) xi=xi+boxxsize + yi=dmod(yi,boxysize) + if (yi.lt.0.0d0) yi=yi+boxysize + zi=dmod(zi,boxzsize) + if (zi.lt.0.0d0) zi=zi+boxzsize + return + end subroutine to_box +!-------------------------------------------------------------------------- + subroutine lipid_layer(xi,yi,zi,sslipi,ssgradlipi) + implicit none +! include 'DIMENSIONS' +! include 'COMMON.IOUNITS' +! include 'COMMON.CHAIN' + double precision xi,yi,zi,sslipi,ssgradlipi + double precision fracinbuf +! double precision sscalelip,sscagradlip +#ifdef DEBUG + write (iout,*) "bordlipbot",bordlipbot," bordliptop",bordliptop + write (iout,*) "buflipbot",buflipbot," lipbufthick",lipbufthick + write (iout,*) "xi yi zi",xi,yi,zi +#endif + if ((zi.gt.bordlipbot).and.(zi.lt.bordliptop)) then +! the energy transfer exist + if (zi.lt.buflipbot) then +! what fraction I am in + fracinbuf=1.0d0-((zi-bordlipbot)/lipbufthick) +! lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zi.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0 + endif +#ifdef DEBUG + write (iout,*) "sslipi",sslipi," ssgradlipi",ssgradlipi +#endif + return + end subroutine lipid_layer +!------------------------------------------------------------- + subroutine ecat_prot_transition(ecation_prottran) + integer:: itypi,itypj,ityptrani,ityptranj,k,l,i,j + real(kind=8),dimension(3):: cjtemp,citemp,diff,dsctemp,vecsc,& + diffnorm,boxx,r,dEvan1Cm,dEvan2Cm,dEtotalCm + real(kind=8):: ecation_prottran,dista,sdist,De,ene,x0left,& + alphac,grad,sumvec,simplesum,pom,erdxi,facd1,& + sss_ele_cut,sss_ele_cut_grad,sss2min,sss2mingrad,& + ene1,ene2,grad1,grad2,evan1,evan2,rcal,r4,r7,r0p,& + r06,r012,epscalc,rocal,ract + ecation_prottran=0.0d0 + boxx(1)=boxxsize + boxx(2)=boxysize + boxx(3)=boxzsize + write(iout,*) "start ecattran",g_listcatsctran_start,g_listcatsctran_end + do k=g_listcatsctran_start,g_listcatsctran_end + i=newcontlistcatsctrani(k) + j=newcontlistcatsctranj(k) +! print *,i,j,"in new tran" + do l=1,3 + citemp(l)=c(l,i+nres) + cjtemp(l)=c(l,j) + enddo + + itypi=itype(i,1) !as the first is the protein part + itypj=itype(j,5) !as the second part is always cation +! remapping to internal types +! read (iiontran,*,err=123,end=123) (agamacattran(k,j,i),k=1,3),& +! (athetacattran(k,j,i),k=1,6),acatshiftdsc(j,i),bcatshiftdsc(j,i),& +! demorsecat(j,i),alphamorsecat(j,i),x0catleft(j,i),x0catright(j,i),& +! x0cattrans(j,i) + + if (itypj.eq.6) then + ityptranj=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani=1 + elseif (itypi.eq.1) then + ityptrani=2 + elseif (itypi.eq.15) then + ityptrani=3 + elseif (itypi.eq.17) then + ityptrani=4 + elseif (itypi.eq.2) then + ityptrani=5 + else + ityptrani=6 + endif + + if (ityptrani.gt.ntrantyp(ityptranj)) then +! do l=1,3 +! write(iout,*),gradcattranc(l,j),gradcattranx(l,i) +! enddo +!volume excluded + call to_box(cjtemp(1),cjtemp(2),cjtemp(3)) + call to_box(citemp(1),citemp(2),citemp(3)) + rcal=0.0d0 + do l=1,3 + r(l)=boxshift(cjtemp(l)-citemp(l),boxx(l)) + rcal=rcal+r(l)*r(l) + enddo + ract=sqrt(rcal) + if (ract.gt.r_cut_ele) cycle + sss_ele_cut=sscale_ele(ract) + sss_ele_cut_grad=sscagrad_ele(ract) + 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 l=1,3 + dEvan1Cm(l) = 12*r(l)*epscalc*r012/r7 + dEvan2Cm(l) = 12*r(l)*epscalc*r06/r4 + enddo + do l=1,3 + dEtotalCm(l)=(dEvan1Cm(l)+dEvan2Cm(l))*sss_ele_cut-& + (Evan1+Evan2)*sss_ele_cut_grad*r(l)/ract + enddo + ecation_prottran = ecation_prottran+& + (Evan1+Evan2)*sss_ele_cut + do l=1,3 + gradcattranx(l,i)=gradcattranx(l,i)+dEtotalCm(l) + gradcattranc(l,i)=gradcattranc(l,i)+dEtotalCm(l) + gradcattranc(l,j)=gradcattranc(l,j)-dEtotalCm(l) + enddo + + ene=0.0d0 + else +! cycle + sumvec=0.0d0 + simplesum=0.0d0 + do l=1,3 + vecsc(l)=citemp(l)-c(l,i) + sumvec=sumvec+vecsc(l)**2 + simplesum=simplesum+vecsc(l) + enddo + sumvec=dsqrt(sumvec) + call to_box(cjtemp(1),cjtemp(2),cjtemp(3)) + call to_box(citemp(1),citemp(2),citemp(3)) +! sumvec=2.0d0 + do l=1,3 + dsctemp(l)=c(l,i+nres)& + +(acatshiftdsc(ityptrani,ityptranj)-1.0d0)*vecsc(l)& + +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec + enddo + call to_box(dsctemp(1),dsctemp(2),dsctemp(3)) + sdist=0.0d0 + do l=1,3 + diff(l)=boxshift(dsctemp(l)-cjtemp(l),boxx(l)) + sdist=sdist+diff(l)*diff(l) + enddo + dista=sqrt(sdist) + if (dista.gt.r_cut_ele) cycle + + sss_ele_cut=sscale_ele(dista) + sss_ele_cut_grad=sscagrad_ele(dista) + sss2min=sscale2(dista,x0cattrans(ityptrani,ityptranj)-0.1d0,0.2d0) + De=demorsecat(ityptrani,ityptranj) + alphac=alphamorsecat(ityptrani,ityptranj) + if (sss2min.eq.1.0d0) then +! print *,"ityptrani",ityptrani,ityptranj + x0left=x0catleft(ityptrani,ityptranj) ! to mn + ene=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2) + grad=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*& + (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut& + +ene/sss_ele_cut*sss_ele_cut_grad + else if (sss2min.eq.0.0d0) then + x0left=x0catright(ityptrani,ityptranj) + ene=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2) + grad=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*& + (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut& + +ene/sss_ele_cut*sss_ele_cut_grad + else + sss2mingrad=sscagrad2(dista,x0cattrans(ityptrani,ityptranj)-0.1d0,0.2d0) + x0left=x0catleft(ityptrani,ityptranj) + ene1=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2) + grad1=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*& + (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut& + +ene/sss_ele_cut*sss_ele_cut_grad + x0left=x0catright(ityptrani,ityptranj) + ene2=sss_ele_cut*(-De+De*(1.0d0-dexp(-alphac*(dista-x0left)))**2) + grad2=2.0d0*alphac*De*dexp(-alphac*(dista-x0left))*& + (1.0d0-dexp(-alphac*(dista-x0left)))*sss_ele_cut& + +ene/sss_ele_cut*sss_ele_cut_grad + ene=sss2min*ene1+(1.0d0-sss2min)*ene2 + grad=sss2min*grad1+(1.0d0-sss2min)*grad2+sss2mingrad*(ene1-ene2) + endif + do l=1,3 + diffnorm(l)= diff(l)/dista + enddo + erdxi=scalar(diffnorm(1),dc_norm(1,i+nres)) + facd1=bcatshiftdsc(ityptrani,ityptranj)/sumvec + + do l=1,3 +! DO k= 1, 3 +! ertail(k) = Rtail_distance(k)/Rtail +! END DO +! erdxi = scalar( ertail(1), dC_norm(1,i+nres) ) +! erdxj = scalar( ertail(1), dC_norm(1,j+nres) ) +! facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres) +! facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres) +! DO k = 1, 3 +!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) +! pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) +! gvdwx(k,i) = gvdwx(k,i) & +! - (( dFdR + gg(k) ) * pom) + pom=diffnorm(l)+facd1*(diffnorm(l)-erdxi*dc_norm(l,i+nres)) +! write(iout,*),gradcattranc(l,j),gradcattranx(l,i),grad*diff(l)/dista + + gradcattranx(l,i)=gradcattranx(l,i)+grad*pom& + +grad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0) +! *( bcatshiftdsc(ityptrani,ityptranj)*& +! (1.0d0/sumvec-(vecsc(l)*simplesum)*(sumvec**(-3.0d0)))) + gradcattranc(l,i)=gradcattranc(l,i)+grad*diff(l)/dista +! +sss_ele_cut_grad*ene*diff(l)/dista/sss_ele_cut + gradcattranc(l,j)=gradcattranc(l,j)-grad*diff(l)/dista +! -sss_ele_cut_grad*ene*diff(l)/dista/sss_ele_cut + enddo + ecation_prottran=ecation_prottran+ene + if (energy_dec) write(iout,*) "etrancat",i,j,ene,x0left,De,dista,& + alphac + endif + enddo +! do k=g_listcatptran_start,g_listcatptran_end +! ene=0.0d0 this will be used if peptide group interaction is needed +! enddo + + + return + end subroutine + subroutine ecat_prot_ang(ecation_protang) + integer:: itypi,itypj,ityptrani,ityptranj,k,l,i,j,n,m,& + ityptrani1,ityptranj1,ityptrani2,ityptranj2,& + i1,i2,j1,j2,k1,k2,k3,i3,j3,ityptrani3,ityptranj3 + + real(kind=8),dimension(3):: cjtemp,citemp,diff,dsctemp,vecsc,& + diffnorm,boxx,dscvec,dscvecnorm,diffnorm2,& + dscvec2,dscvecnorm2,cjtemp2,citemp2,diff2,dsctemp2,& + vecsc2,diff1,diffnorm1,diff3,mindiffnorm2 + real(kind=8),dimension(3):: dscvec1,dscvecnorm1,cjtemp1,citemp1,vecsc1,dsctemp1,& + dscvec3,dscvecnorm3,cjtemp3,citemp3,vecsc3,dsctemp3,& + diffnorm3,diff4,diffnorm4 + + real(kind=8):: ecation_protang,dista,sdist,De,ene,x0left,& + alphac,grad,sumvec,sumdscvec,pom,erdxi,facd1,& + sss_ele_cut,sss_ele_cut_grad,sss2min,sss2mingrad,& + simplesum,cosval,part1,part2a,part2,part2b,part3,& + part4a,part4b,part4,bottom,dista2,sdist2,sumvec2,& + sumdscvec2,simplesum2,dista1,sdist1,sumvec1,simplesum1,& + sumdscvec1,facd2,scal1a,scal1b,scal2a,scal2b,& + sss2mingrad1,sss2mingrad2,sss2min1,sss2min2,pom1,pom2,& + det1ij,det2ij,cosom1,cosom2,cosom12,cosphij,dista3,& + sumvec3 + real(kind=8):: sinom1,sinom2,sinaux,dephiij,sumdscvec3,sumscvec3,& + cosphi,sdist3,simplesum3,det1t2ij,sss2mingrad3,sss2min3,& + scal1c,scal2c,scal3a,scal3b,scal3c,facd3,facd2b,scal3d,& + scal3e,dista4,sdist4,pom3,sssmintot + + ecation_protang=0.0d0 + boxx(1)=boxxsize + boxx(2)=boxysize + boxx(3)=boxzsize +! print *,"KUR**3",g_listcatscang_start,g_listcatscang_end +! go to 19 +! go to 21 + do k=g_listcatscang_start,g_listcatscang_end + ene=0.0d0 + i=newcontlistcatscangi(k) + j=newcontlistcatscangj(k) + itypi=itype(i,1) !as the first is the protein part + itypj=itype(j,5) !as the second part is always cation +! print *,"KUR**4",i,j,itypi,itypj +! remapping to internal types +! read (iiontran,*,err=123,end=123) (agamacattran(k,j,i),k=1,3),& +! (athetacattran(k,j,i),k=1,6),acatshiftdsc(j,i),bcatshiftdsc(j,i),& +! demorsecat(j,i),alphamorsecat(j,i),x0catleft(j,i),x0catright(j,i),& +! x0cattrans(j,i) + if (itypj.eq.6) then + ityptranj=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani=1 + elseif (itypi.eq.1) then + ityptrani=2 + elseif (itypi.eq.15) then + ityptrani=3 + elseif (itypi.eq.17) then + ityptrani=4 + elseif (itypi.eq.2) then + ityptrani=5 + else + ityptrani=6 + endif + if (ityptrani.gt.ntrantyp(ityptranj)) cycle + do l=1,3 + citemp(l)=c(l,i+nres) + cjtemp(l)=c(l,j) + enddo + sumvec=0.0d0 + simplesum=0.0d0 + do l=1,3 + vecsc(l)=citemp(l)-c(l,i) + sumvec=sumvec+vecsc(l)**2 + simplesum=simplesum+vecsc(l) + enddo + sumvec=dsqrt(sumvec) + sumdscvec=0.0d0 + do l=1,3 + dsctemp(l)=c(l,i)& +! +1.0d0 + +(acatshiftdsc(ityptrani,ityptranj))*vecsc(l)& + +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec + dscvec(l)= & +!1.0d0 + (acatshiftdsc(ityptrani,ityptranj))*vecsc(l)& + +bcatshiftdsc(ityptrani,ityptranj)*vecsc(l)/sumvec + sumdscvec=sumdscvec+dscvec(l)**2 + enddo + sumdscvec=dsqrt(sumdscvec) + do l=1,3 + dscvecnorm(l)=dscvec(l)/sumdscvec + enddo + call to_box(dsctemp(1),dsctemp(2),dsctemp(3)) + call to_box(cjtemp(1),cjtemp(2),cjtemp(3)) + sdist=0.0d0 + do l=1,3 + diff(l)=boxshift(dsctemp(l)-cjtemp(l),boxx(l)) + sdist=sdist+diff(l)*diff(l) + enddo + dista=sqrt(sdist) + do l=1,3 + diffnorm(l)= diff(l)/dista + enddo + cosval=scalar(diffnorm(1),dc_norm(1,i+nres)) + grad=0.0d0 + sss2min=sscale2(dista,r_cut_ang,1.0d0) + sss2mingrad=sscagrad2(dista,r_cut_ang,1.0d0) + ene=ene& + +tschebyshev(1,6,athetacattran(1,ityptrani,ityptranj),cosval) + grad=gradtschebyshev(0,5,athetacattran(1,ityptrani,ityptranj),cosval)*sss2min + + facd1=bcatshiftdsc(ityptrani,ityptranj)/sumvec + erdxi=scalar(diffnorm(1),dc_norm(1,i+nres)) + part1=0.0d0 + part2=0.0d0 + part3=0.0d0 + part4=0.0d0 + do l=1,3 + bottom=sumvec**2*sdist + part1=diff(l)*sumvec*dista + part2a=(acatshiftdsc(ityptrani,ityptranj))*vecsc(l) + part2b=0.0d0 + !bcatshiftdsc(ityptrani,ityptranj)/sumvec*& + !(vecsc(l)-cosval*dista*dc_norm(l,i+nres)) + part2=(part2a+part2b)*sumvec*dista + part3=cosval*sumvec*dista*dc_norm(l,i+nres)*dista + part4a=diff(l)*acatshiftdsc(ityptrani,ityptranj) + part4b=bcatshiftdsc(ityptrani,ityptranj)/sumvec*& + (diff(l)-cosval*dista*dc_norm(l,i+nres)) + part4=cosval*sumvec*(part4a+part4b)*sumvec +! gradlipang(m,l)=gradlipang(m,l)+(fac & +! *(xa(m)-scalar*vnorm*xb(m)/wnorm)& +! /(vnorm*wnorm)) + +! DO k= 1, 3 +! ertail(k) = Rtail_distance(k)/Rtail +! END DO +! erdxi = scalar( ertail(1), dC_norm(1,i+nres) ) +! erdxj = scalar( ertail(1), dC_norm(1,j+nres) ) +! facd1 = dtail(1,itypi,itypj) * vbld_inv(i+nres) +! facd2 = dtail(2,itypi,itypj) * vbld_inv(j+nres) +! DO k = 1, 3 +!c! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i) +!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j) +! pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) +! gvdwx(k,i) = gvdwx(k,i) & +! - (( dFdR + gg(k) ) * pom) + pom=diffnorm(l)+facd1*(diffnorm(l)-erdxi*dc_norm(l,i+nres)) + + gradcatangc(l,j)=gradcatangc(l,j)-grad*& + (dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)-& + ene*sss2mingrad*diffnorm(l) + + gradcatangc(l,i)=gradcatangc(l,i)+grad*& + (dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)+& + ene*sss2mingrad*diffnorm(l) + + gradcatangx(l,i)=gradcatangx(l,i)+grad*& + (part1+part2-part3-part4)/bottom+& + ene*sss2mingrad*pom+& + ene*sss2mingrad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0) +! +grad*(dscvec(l)-cosval*diffnorm(l)*sumdscvec)/(sumdscvec*dista)& +! +grad*pom+grad*diffnorm(l)*(acatshiftdsc(ityptrani,ityptranj)-1.0d0) +!& +! (diff(l)-cosval*dscvecnorm(l)*dista)/(sumdscvec*dista) + + + + + + enddo +! print *,i,j,cosval,tschebyshev(1,3,aomicattr(1,ityptranj),cosval)& +! ,aomicattr(0,ityptranj),ene + if (energy_dec) write(iout,*) i,j,ityptrani,ityptranj,ene,cosval + ecation_protang=ecation_protang+ene*sss2min + enddo + 19 continue +! print *,"KUR**",g_listcatscangf_start,g_listcatscangf_end + do k=g_listcatscangf_start,g_listcatscangf_end + ene=0.0d0 + i1=newcontlistcatscangfi(k) + j1=newcontlistcatscangfj(k) + itypi=itype(i1,1) !as the first is the protein part + itypj=itype(j1,5) !as the second part is always cation + if (itypj.eq.6) then + ityptranj1=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani1=1 + elseif (itypi.eq.1) then + ityptrani1=2 + elseif (itypi.eq.15) then + ityptrani1=3 + elseif (itypi.eq.17) then + ityptrani1=4 + elseif (itypi.eq.2) then + ityptrani1=5 + else + ityptrani1=6 + endif + do l=1,3 + citemp1(l)=c(l,i1+nres) + cjtemp1(l)=c(l,j1) + enddo + sumvec1=0.0d0 + simplesum1=0.0d0 + do l=1,3 + vecsc1(l)=citemp1(l)-c(l,i1) + sumvec1=sumvec1+vecsc1(l)**2 + simplesum1=simplesum1+vecsc1(l) + enddo + sumvec1=dsqrt(sumvec1) + sumdscvec1=0.0d0 + do l=1,3 + dsctemp1(l)=c(l,i1)& +! +1.0d0 + +(acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)& + +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1 + dscvec1(l)= & +!1.0d0 + (acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)& + +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1 + sumdscvec1=sumdscvec1+dscvec1(l)**2 + enddo + sumdscvec1=dsqrt(sumdscvec1) + do l=1,3 + dscvecnorm1(l)=dscvec1(l)/sumdscvec1 + enddo + call to_box(dsctemp1(1),dsctemp1(2),dsctemp1(3)) + call to_box(cjtemp1(1),cjtemp1(2),cjtemp1(3)) + sdist1=0.0d0 + do l=1,3 + diff1(l)=boxshift(dsctemp1(l)-cjtemp1(l),boxx(l)) + sdist1=sdist1+diff1(l)*diff1(l) + enddo + dista1=sqrt(sdist1) + do l=1,3 + diffnorm1(l)= diff1(l)/dista1 + enddo + sss2min1=sscale2(dista1,r_cut_ang,1.0d0) + sss2mingrad1=sscagrad2(dista1,r_cut_ang,1.0d0) + if (ityptrani1.gt.ntrantyp(ityptranj1)) cycle + +!----------------------------------------------------------------- +! do m=k+1,g_listcatscang_end + ene=0.0d0 + i2=newcontlistcatscangfk(k) + j2=j1 + if (j1.ne.j2) cycle + itypi=itype(i2,1) !as the first is the protein part + itypj=itype(j2,5) !as the second part is always cation + if (itypj.eq.6) then + ityptranj2=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani2=1 + elseif (itypi.eq.1) then + ityptrani2=2 + elseif (itypi.eq.15) then + ityptrani2=3 + elseif (itypi.eq.17) then + ityptrani2=4 + elseif (itypi.eq.2) then + ityptrani2=5 + else + ityptrani2=6 + endif + if (ityptrani2.gt.ntrantyp(ityptranj2)) cycle + + do l=1,3 + citemp2(l)=c(l,i2+nres) + cjtemp2(l)=c(l,j2) + enddo + sumvec2=0.0d0 + simplesum2=0.0d0 + do l=1,3 + vecsc2(l)=citemp2(l)-c(l,i2) + sumvec2=sumvec2+vecsc2(l)**2 + simplesum2=simplesum2+vecsc2(l) + enddo + sumvec2=dsqrt(sumvec2) + sumdscvec2=0.0d0 + do l=1,3 + dsctemp2(l)=c(l,i2)& +! +1.0d0 + +(acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)& + +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2 + dscvec2(l)= & +!1.0d0 + (acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)& + +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2 + sumdscvec2=sumdscvec2+dscvec2(l)**2 + enddo + sumdscvec2=dsqrt(sumdscvec2) + do l=1,3 + dscvecnorm2(l)=dscvec2(l)/sumdscvec2 + enddo + call to_box(dsctemp2(1),dsctemp2(2),dsctemp2(3)) + call to_box(cjtemp2(1),cjtemp2(2),cjtemp2(3)) + sdist2=0.0d0 + do l=1,3 + diff2(l)=boxshift(dsctemp2(l)-cjtemp2(l),boxx(l)) +! diff2(l)=1.0d0 + sdist2=sdist2+diff2(l)*diff2(l) + enddo + dista2=sqrt(sdist2) + do l=1,3 + diffnorm2(l)= diff2(l)/dista2 + enddo +! print *,i1,i2,diffnorm2(1) + cosval=scalar(diffnorm1(1),diffnorm2(1)) + grad=0.0d0 + sss2min2=sscale2(dista2,r_cut_ang,1.0d0) + sss2mingrad2=sscagrad2(dista2,r_cut_ang,1.0d0) + ene=ene+tschebyshev(1,3,aomicattr(1,ityptranj1),cosval) + grad=gradtschebyshev(0,2,aomicattr(1,ityptranj1),cosval)*sss2min2*sss2min1 + part1=0.0d0 + part2=0.0d0 + part3=0.0d0 + part4=0.0d0 + ecation_protang=ecation_protang+ene*sss2min2*sss2min1 + facd1=bcatshiftdsc(ityptrani1,ityptranj1)/sumvec1 + facd2=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec2 + scal1a=scalar(diffnorm1(1),dc_norm(1,i1+nres)) + scal1b=scalar(diffnorm2(1),dc_norm(1,i1+nres)) + scal2a=scalar(diffnorm1(1),dc_norm(1,i2+nres)) + scal2b=scalar(diffnorm2(1),dc_norm(1,i2+nres)) + + if (energy_dec) write(iout,*) "omi", i,j,ityptrani,ityptranj,ene,cosval,aomicattr(1,ityptranj1),& + aomicattr(2,ityptranj1),aomicattr(3,ityptranj1),tschebyshev(1,3,aomicattr(1,ityptranj1),cosval) + +!*sss2min + do l=1,3 + pom1=diffnorm1(l)+facd1*(diffnorm1(l)-scal1a*dc_norm(l,i1+nres)) + pom2=diffnorm2(l)+facd2*(diffnorm2(l)-scal2b*dc_norm(l,i2+nres)) + + + gradcatangc(l,i1)=gradcatangc(l,i1)+grad*(diff2(l)-& + cosval*diffnorm1(l)*dista2)/(dista2*dista1)+& + ene*sss2mingrad1*diffnorm1(l)*sss2min2 + + + gradcatangx(l,i1)=gradcatangx(l,i1)+grad/(dista2*dista1)*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff2(l)+& + facd1*(diff2(l)-scal1b*dc_norm(l,i1+nres)*dista2)-& + cosval*dista2/dista1*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+& + facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1)))+& + ene*sss2mingrad1*sss2min2*(pom1+& + diffnorm1(l)*(acatshiftdsc(ityptrani1,ityptranj1)-1.0d0)) + + + gradcatangx(l,i2)=gradcatangx(l,i2)+grad/(dista2*dista1)*& + (acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)+& + facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1)-& + cosval*dista1/dista2*& + (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+& + facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)))+& + ene*sss2mingrad2*sss2min1*(pom2+& + diffnorm2(l)*(acatshiftdsc(ityptrani2,ityptranj2)-1.0d0)) + + + gradcatangx(l,i2)=gradcatangx(l,i2) + gradcatangc(l,i2)=gradcatangc(l,i2)+grad*(diff1(l)-& + cosval*diffnorm2(l)*dista1)/(dista2*dista1)+& + ene*sss2mingrad2*diffnorm2(l)*sss2min1 + + gradcatangc(l,j2)=gradcatangc(l,j2)-grad*(diff2(l)/dista2/dista1-& + cosval*diff1(l)/dista1/dista1+diff1(l)/dista2/dista1-& + cosval*diff2(l)/dista2/dista2)-& + ene*sss2mingrad1*diffnorm1(l)*sss2min2-& + ene*sss2mingrad2*diffnorm2(l)*sss2min1 + + + enddo + + enddo +! enddo +!#ifdef DUBUG + 21 continue +! do k1=g_listcatscang_start,g_listcatscang_end +! print *,"KURNA",g_listcatscangt_start,g_listcatscangt_end + do k1=g_listcatscangt_start,g_listcatscangt_end + i1=newcontlistcatscangti(k1) + j1=newcontlistcatscangtj(k1) + itypi=itype(i1,1) !as the first is the protein part + itypj=itype(j1,5) !as the second part is always cation + if (itypj.eq.6) then + ityptranj1=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani1=1 + elseif (itypi.eq.1) then + ityptrani1=2 + elseif (itypi.eq.15) then + ityptrani1=3 + elseif (itypi.eq.17) then + ityptrani1=4 + elseif (itypi.eq.2) then + ityptrani1=5 + else + ityptrani1=6 + endif + do l=1,3 + citemp1(l)=c(l,i1+nres) + cjtemp1(l)=c(l,j1) + enddo + sumvec1=0.0d0 + simplesum1=0.0d0 + do l=1,3 + vecsc1(l)=citemp1(l)-c(l,i1) + sumvec1=sumvec1+vecsc1(l)**2 + simplesum1=simplesum1+vecsc1(l) + enddo + sumvec1=dsqrt(sumvec1) + sumdscvec1=0.0d0 + do l=1,3 + dsctemp1(l)=c(l,i1)& + +(acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)& + +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1 + dscvec1(l)= & + (acatshiftdsc(ityptrani1,ityptranj1))*vecsc1(l)& + +bcatshiftdsc(ityptrani1,ityptranj1)*vecsc1(l)/sumvec1 + sumdscvec1=sumdscvec1+dscvec1(l)**2 + enddo + sumdscvec1=dsqrt(sumdscvec1) + do l=1,3 + dscvecnorm1(l)=dscvec1(l)/sumdscvec1 + enddo + call to_box(dsctemp1(1),dsctemp1(2),dsctemp1(3)) + call to_box(cjtemp1(1),cjtemp1(2),cjtemp1(3)) + sdist1=0.0d0 + do l=1,3 + diff1(l)=boxshift(dsctemp1(l)-cjtemp1(l),boxx(l)) + sdist1=sdist1+diff1(l)*diff1(l) + enddo + dista1=sqrt(sdist1) + do l=1,3 + diffnorm1(l)= diff1(l)/dista1 + enddo + sss2min1=sscale2(dista1,r_cut_ang,1.0d0) + sss2mingrad1=sscagrad2(dista1,r_cut_ang,1.0d0) + if (ityptrani1.gt.ntrantyp(ityptranj1)) cycle +!---------------before second loop +! do k2=k1+1,g_listcatscang_end + i2=newcontlistcatscangtk(k1) + j2=j1 +! print *,"TUTU3",i1,i2,j1,j2 + if (i2.eq.i1) cycle + if (j2.ne.j1) cycle + itypi=itype(i2,1) !as the first is the protein part + itypj=itype(j2,5) !as the second part is always cation + if (itypj.eq.6) then + ityptranj2=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani2=1 + elseif (itypi.eq.1) then + ityptrani2=2 + elseif (itypi.eq.15) then + ityptrani2=3 + elseif (itypi.eq.17) then + ityptrani2=4 + elseif (itypi.eq.2) then + ityptrani2=5 + else + ityptrani2=6 + endif + if (ityptrani2.gt.ntrantyp(ityptranj2)) cycle + do l=1,3 + citemp2(l)=c(l,i2+nres) + cjtemp2(l)=c(l,j2) + enddo + sumvec2=0.0d0 + simplesum2=0.0d0 + do l=1,3 + vecsc2(l)=citemp2(l)-c(l,i2) + sumvec2=sumvec2+vecsc2(l)**2 + simplesum2=simplesum2+vecsc2(l) + enddo + sumvec2=dsqrt(sumvec2) + sumdscvec2=0.0d0 + do l=1,3 + dsctemp2(l)=c(l,i2)& + +(acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)& + +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2 + dscvec2(l)= & + (acatshiftdsc(ityptrani2,ityptranj2))*vecsc2(l)& + +bcatshiftdsc(ityptrani2,ityptranj2)*vecsc2(l)/sumvec2 + sumdscvec2=sumdscvec2+dscvec2(l)**2 + enddo + sumdscvec2=dsqrt(sumdscvec2) + do l=1,3 + dscvecnorm2(l)=dscvec2(l)/sumdscvec2 + enddo + call to_box(dsctemp2(1),dsctemp2(2),dsctemp2(3)) + call to_box(cjtemp2(1),cjtemp2(2),cjtemp2(3)) + sdist2=0.0d0 + do l=1,3 + diff2(l)=boxshift(dsctemp2(l)-cjtemp2(l),boxx(l)) +! diff2(l)=1.0d0 + sdist2=sdist2+diff2(l)*diff2(l) + enddo + dista2=sqrt(sdist2) + do l=1,3 + diffnorm2(l)= diff2(l)/dista2 + mindiffnorm2(l)=-diffnorm2(l) + enddo +! print *,i1,i2,diffnorm2(1) + cosom1=scalar(diffnorm1(1),diffnorm2(1)) + sss2min2=sscale2(dista2,r_cut_ang,1.0d0) + sss2mingrad2=sscagrad2(dista2,r_cut_ang,1.0d0) + +!---------------- before third loop +! do k3=g_listcatscang_start,g_listcatscang_end + ene=0.0d0 + i3=newcontlistcatscangtl(k1) + j3=j1 +! print *,"TUTU4",i1,i2,i3,j1,j2,j3 + + if (i3.eq.i2) cycle + if (i3.eq.i1) cycle + if (j3.ne.j1) cycle + itypi=itype(i3,1) !as the first is the protein part + itypj=itype(j3,5) !as the second part is always cation + if (itypj.eq.6) then + ityptranj3=1 !as now only Zn2+ is this needs to be modified for other ions + endif + if (itypi.eq.16) then + ityptrani3=1 + elseif (itypi.eq.1) then + ityptrani3=2 + elseif (itypi.eq.15) then + ityptrani3=3 + elseif (itypi.eq.17) then + ityptrani3=4 + elseif (itypi.eq.2) then + ityptrani3=5 + else + ityptrani3=6 + endif + if (ityptrani3.gt.ntrantyp(ityptranj3)) cycle + do l=1,3 + citemp3(l)=c(l,i3+nres) + cjtemp3(l)=c(l,j3) + enddo + sumvec3=0.0d0 + simplesum3=0.0d0 + do l=1,3 + vecsc3(l)=citemp3(l)-c(l,i3) + sumvec3=sumvec3+vecsc3(l)**2 + simplesum3=simplesum3+vecsc3(l) + enddo + sumvec3=dsqrt(sumvec3) + sumdscvec3=0.0d0 + do l=1,3 + dsctemp3(l)=c(l,i3)& + +(acatshiftdsc(ityptrani3,ityptranj3))*vecsc3(l)& + +bcatshiftdsc(ityptrani3,ityptranj3)*vecsc3(l)/sumvec3 + dscvec3(l)= & + (acatshiftdsc(ityptrani3,ityptranj3))*vecsc3(l)& + +bcatshiftdsc(ityptrani3,ityptranj3)*vecsc3(l)/sumvec3 + sumdscvec3=sumdscvec3+dscvec3(l)**2 + enddo + sumdscvec3=dsqrt(sumdscvec3) + do l=1,3 + dscvecnorm3(l)=dscvec3(l)/sumdscvec3 + enddo + call to_box(dsctemp3(1),dsctemp3(2),dsctemp3(3)) + call to_box(cjtemp3(1),cjtemp3(2),cjtemp3(3)) + sdist3=0.0d0 + do l=1,3 + diff3(l)=boxshift(dsctemp3(l)-dsctemp2(l),boxx(l)) + sdist3=sdist3+diff3(l)*diff3(l) + enddo + dista3=sqrt(sdist3) + do l=1,3 + diffnorm3(l)= diff3(l)/dista3 + enddo + sdist4=0.0d0 + do l=1,3 + diff4(l)=boxshift(dsctemp3(l)-cjtemp2(l),boxx(l)) +! diff2(l)=1.0d0 + sdist4=sdist4+diff4(l)*diff4(l) + enddo + dista4=sqrt(sdist4) + do l=1,3 + diffnorm4(l)= diff4(l)/dista4 + enddo + + sss2min3=sscale2(dista4,r_cut_ang,1.0d0) + sss2mingrad3=sscagrad2(dista4,r_cut_ang,1.0d0) + sssmintot=sss2min3*sss2min2*sss2min1 + if (ityptrani3.gt.ntrantyp(ityptranj3)) cycle + cosom12=scalar(diffnorm3(1),diffnorm1(1)) + cosom2=scalar(diffnorm3(1),mindiffnorm2(1)) + sinom1=dsqrt(1.0d0-cosom1*cosom1) + sinom2=dsqrt(1.0d0-cosom2*cosom2) + cosphi=cosom12-cosom1*cosom2 + sinaux=sinom1*sinom2 + ene=ene+mytschebyshev(1,3,agamacattran(1,ityptrani2,ityptranj2),cosphi,sinaux) + call mygradtschebyshev(1,3,agamacattran(1,ityptrani2,ityptranj2)& + ,cosphi,sinaux,dephiij,det1t2ij) + + det1ij=-det1t2ij*sinom2*cosom1/sinom1-dephiij*cosom2 + det2ij=-det1t2ij*sinom1*cosom2/sinom2-dephiij*cosom1 + facd1=bcatshiftdsc(ityptrani1,ityptranj1)/sumvec1 + facd2=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec2 +! facd2b=bcatshiftdsc(ityptrani2,ityptranj2)/sumvec3 + facd3=bcatshiftdsc(ityptrani3,ityptranj3)/sumvec3 + scal1a=scalar(diffnorm1(1),dc_norm(1,i1+nres)) + scal1b=scalar(diffnorm2(1),dc_norm(1,i1+nres)) + scal1c=scalar(diffnorm3(1),dc_norm(1,i1+nres)) + scal2a=scalar(diffnorm1(1),dc_norm(1,i2+nres)) + scal2b=scalar(diffnorm2(1),dc_norm(1,i2+nres)) + scal2c=scalar(diffnorm3(1),dc_norm(1,i2+nres)) + scal3a=scalar(diffnorm1(1),dc_norm(1,i3+nres)) + scal3b=scalar(mindiffnorm2(1),dc_norm(1,i3+nres)) + scal3d=scalar(diffnorm2(1),dc_norm(1,i3+nres)) + scal3c=scalar(diffnorm3(1),dc_norm(1,i3+nres)) + scal3e=scalar(diffnorm4(1),dc_norm(1,i3+nres)) + + + do l=1,3 + pom1=diffnorm1(l)+facd1*(diffnorm1(l)-scal1a*dc_norm(l,i1+nres)) + pom2=diffnorm2(l)+facd2*(diffnorm2(l)-scal2b*dc_norm(l,i2+nres)) + pom3=diffnorm4(l)+facd3*(diffnorm4(l)-scal3e*dc_norm(l,i3+nres)) + + gradcatangc(l,i1)=gradcatangc(l,i1)& + +det1ij*sssmintot*(diff2(l)-diffnorm1(l)*cosom1*dista2)/(dista2*dista1)+& + dephiij*sssmintot*(diff3(l)-diffnorm1(l)*cosom12*dista3)/(dista3*dista1)& + +ene*sss2mingrad1*diffnorm1(l)*sss2min2*sss2min3 + + + gradcatangc(l,i2)=gradcatangc(l,i2)+(& + det1ij*(diff1(l)-diffnorm2(l)*cosom1*dista1)/(dista2*dista1)+& + det2ij*(-diff3(l)+mindiffnorm2(l)*cosom2*dista3)/(dista3*dista2)& + -det2ij*(-diff2(l)-diffnorm3(l)*cosom2*dista2)/(dista3*dista2)& + -dephiij*(diff1(l)-diffnorm3(l)*cosom12*dista1)/(dista3*dista1))*sssmintot& + +ene*sss2mingrad2*diffnorm2(l)*sss2min1*sss2min3 + + + + gradcatangc(l,i3)=gradcatangc(l,i3)& + +det2ij*(-diff2(l)-diffnorm3(l)*cosom2*dista2)/(dista3*dista2)*sssmintot& + +dephiij*(diff1(l)-diffnorm3(l)*cosom12*dista1)/(dista3*dista1)*sssmintot& + +ene*sss2mingrad3*diffnorm4(l)*sss2min1*sss2min2 + + + gradcatangc(l,j1)=gradcatangc(l,j1)-& + sssmintot*(det1ij*(diff2(l)-diffnorm1(l)*cosom1*dista2)/(dista2*dista1)+& + dephiij*(diff3(l)-diffnorm1(l)*cosom12*dista3)/(dista3*dista1))& + -(det1ij*(diff1(l)-diffnorm2(l)*cosom1*dista1)/(dista1*dista2)+& + det2ij*(-diff3(l)+mindiffnorm2(l)*cosom2*dista3)/(dista3*dista2))*sssmintot& + -ene*sss2mingrad1*diffnorm1(l)*sss2min2*sss2min3& + -ene*sss2mingrad2*diffnorm2(l)*sss2min1*sss2min3& + -ene*sss2mingrad3*diffnorm4(l)*sss2min1*sss2min2 + + + gradcatangx(l,i1)=gradcatangx(l,i1)+(det1ij/(dista2*dista1)*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff2(l)+& + facd1*(diff2(l)-scal1b*dc_norm(l,i1+nres)*dista2)-& + cosom1*dista2/dista1*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+& + facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1)))& + +dephiij/(dista3*dista1)*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff3(l)+& + facd1*(diff3(l)-scal1c*dc_norm(l,i1+nres)*dista3)-& + cosom12*dista3/dista1*& + (acatshiftdsc(ityptrani1,ityptranj1)*diff1(l)+& + facd1*(diff1(l)-scal1a*dc_norm(l,i1+nres)*dista1))))*sssmintot& + +ene*sss2mingrad1*sss2min2*sss2min3*(pom1+& + diffnorm1(l)*(acatshiftdsc(ityptrani1,ityptranj1)-1.0d0)) + + + gradcatangx(l,i3)=gradcatangx(l,i3)+(& + det2ij/(dista3*dista2)*& + (acatshiftdsc(ityptrani3,ityptranj3)*(-diff2(l))+& + facd3*(-diff2(l)-scal3b*dc_norm(l,i3+nres)*dista2)-& + cosom2*dista2/dista3*& + (acatshiftdsc(ityptrani3,ityptranj3)*diff3(l)+& + facd3*(diff3(l)-scal3c*dc_norm(l,i3+nres)*dista3)))& + +dephiij/(dista3*dista1)*& + (acatshiftdsc(ityptrani3,ityptranj3)*diff1(l)+& + facd3*(diff1(l)-scal3a*dc_norm(l,i3+nres)*dista1)-& + cosom12*dista1/dista3*& + (acatshiftdsc(ityptrani3,ityptranj3)*diff3(l)+& + facd3*(diff3(l)-scal3c*dc_norm(l,i3+nres)*dista3))))*sssmintot& + +ene*sss2mingrad3*sss2min2*sss2min1*(pom3+& + diffnorm4(l)*(acatshiftdsc(ityptrani3,ityptranj3)-1.0d0)) + + + gradcatangx(l,i2)=gradcatangx(l,i2)+(&! + det1ij/(dista2*dista1)*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)&! + +facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1)& + -cosom1*dista1/dista2*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&! + facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)))+& + det2ij/(dista3*dista2)*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&! + facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2)& + -(acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&! + facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3))& + -cosom2*dista3/dista2*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff2(l)+&! + facd2*(diff2(l)-scal2b*dc_norm(l,i2+nres)*dista2))& + +cosom2*dista2/dista3*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&! + facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3)))& + +dephiij/(dista3*dista1)*&! + (-(acatshiftdsc(ityptrani2,ityptranj2)*diff1(l)+&! + facd2*(diff1(l)-scal2a*dc_norm(l,i2+nres)*dista1))+& + cosom12*dista1/dista3*&! + (acatshiftdsc(ityptrani2,ityptranj2)*diff3(l)+&! + facd2*(diff3(l)-scal2c*dc_norm(l,i2+nres)*dista3))))*sssmintot& + +ene*sss2mingrad2*sss2min3*sss2min1*(pom2+& + diffnorm2(l)*(acatshiftdsc(ityptrani2,ityptranj2)-1.0d0)) + + + enddo +! print *,i1,i2,i3,j1,j2,j3,"tors",ene,sinaux,cosphi +! print *,"param",agamacattran(1,ityptrani2,ityptranj2),ityptranj2,ityptrani2 + ecation_protang=ecation_protang+ene*sssmintot + enddo +! enddo +! enddo +!#endif + return + end subroutine +!-------------------------------------------------------------------------- +!c------------------------------------------------------------------------------ + double precision function mytschebyshev(m,n,x,y,yt) + implicit none + integer i,m,n + double precision x(n),y,yt,yy(0:100),aux +!c Tschebyshev polynomial in y multiplied by sin(t1)sin(t2) (yt). +!c Note that the first term is omitted +!c m=0: the constant term is included +!c m=1: the constant term is not included + yy(0)=1.0d0 + yy(1)=y + do i=2,n + yy(i)=2*yy(1)*yy(i-1)-yy(i-2)*yt*yt + enddo + aux=0.0d0 + do i=m,n + aux=aux+x(i)*yy(i) + enddo +!c print *,(yy(i),i=1,n) + mytschebyshev=aux + return + end function +!C-------------------------------------------------------------------------- +!C-------------------------------------------------------------------------- + subroutine mygradtschebyshev(m,n,x,y,yt,fy,fyt) + implicit none + integer i,m,n + double precision x(n+1),y,yt,fy,fyt,yy(0:100),yb(0:100), & + ybt(0:100) +!c Derivative of Tschebyshev polynomial in y multiplied by sin(t1)sin(t2) (yt). +!c Note that the first term is omitted +!c m=0: the constant term is included +!c m=1: the constant term is not included + yy(0)=1.0d0 + yy(1)=y + yb(0)=0.0d0 + yb(1)=1.0d0 + ybt(0)=0.0d0 + ybt(1)=0.0d0 + do i=2,n + yy(i)=2*yy(1)*yy(i-1)-yy(i-2)*yt*yt + yb(i)=2*yy(i-1)+2*yy(1)*yb(i-1)-yb(i-2)*yt*yt + ybt(i)=2*yy(1)*ybt(i-1)-ybt(i-2)*yt*yt-2*yy(i-2)*yt + enddo + fy=0.0d0 + fyt=0.0d0 + do i=m,n + fy=fy+x(i)*yb(i) + fyt=fyt+x(i)*ybt(i) + enddo + return + end subroutine + subroutine fodstep(nsteps) + use geometry_data, only: c, nres, theta, alph + use geometry, only:alpha,beta,dist + integer, intent(in) :: nsteps + integer idxtomod, j, i + double precision RD0, RD1, fi +! double precision alpha +! double precision beta +! double precision dist +! double precision compute_RD + double precision TT + real :: r21(5) +!c ! Założenia: dla łańcucha zapisanego w tablicy c zawierającego +!c ! nres elementów CA i CB da się wyznaczyć kąty płaskie +!c ! theta (procedura Alpha) i kąty torsyjne (procedura beta), +!c ! zapisywane w tablicach theta i alph. +!c ! Na podstawie danych z tych tablic da się odtworzyć +!c ! strukturę 3D łańcucha procedurą chainbuild. +!c ! +! print *,"fodstep: nres=",nres + RD0 = compute_RD() +! print *, "RD0before step: ",RD0 + do j=1,nsteps +!c ! Wyznaczenie kątów theta na podstawie struktury +!c ! zapisanej w tablicy c + do i=3,nres + TT=alpha(i-2,i-1,i) + theta(i)=TT +!c print *,"TT=",TT + end do +!c ! Wyznaczenie kątów phi na podstawie struktury +!c ! zapisanej w tablicy c + do i=4,nres + phi(i)=beta(i-3,i-2,i-1,i) + end do +!c ! Wyznaczenie odległości między atomami +!c ! vbld(i)=dist(i-1,i) + do i=2,nres + vbld(i)=dist(i-1,i) + end do +!c ! losujemy kilka liczb + call random_number(r21) +!c ! r21(1): indeks pozycji do zmiany +!c ! r21(2): kąt (r21(2)/20.0-1/40.0) +!c ! r21(3): wybór tablicy + RD0 = compute_RD() +!c print *, "RD before step: ",RD0 + fi = (r21(2)/20.0-1.0/40.0) ! o tyle radianów zmienimy losowy kąt + if (r21(3) .le. 0.5) then + idxtomod = 3+r21(1)*(nres - 2) + theta(idxtomod) = theta(idxtomod)+fi +! print *,"Zmiana kąta theta(",& +! idxtomod,") o fi = ",fi + else + idxtomod = 4+r21(1)*(nres - 3) + phi(idxtomod) = phi(idxtomod)+fi +! print *,"Zmiana kąta phi(",& +! idxtomod,") o fi = ",fi + end if +!c ! odtwarzamy łańcuch + call chainbuild +!c ! czy coś się polepszyło? + RD1 = compute_RD() + if (RD1 .gt. RD0) then ! nie, wycofujemy zmianę +! print *, "RD after step: ",RD1," rejected" + if (r21(3) .le. 0.5) then + theta(idxtomod) = theta(idxtomod)-fi + else + phi(idxtomod) = phi(idxtomod)-fi + end if + call chainbuild ! odtworzenie pierwotnej wersji (bez zmienionego kąta) + else +! print *, "RD after step: ",RD1," accepted" + continue + end if + end do + end subroutine +!c----------------------------------------------------------------------------------------- + subroutine orientation_matrix(res) ! obliczenie macierzy oraz przygotowanie ea z tymi przeksztalceniami + use geometry_data, only: c, nres + use energy_data, only: itype + double precision, intent(out) :: res(4,4) + double precision resM(4,4) + double precision M(4,4) + double precision M2(4,4) + integer i, j, maxi, maxj +! double precision sq + double precision maxd, dd + double precision v1(3) + double precision v2(3) + double precision vecnea(3) + double precision mean_ea(3) + double precision fi +!c ! liczymy atomy efektywne i zapisujemy w tablicy ea + do i=1,nres +!c if (itype(i,1) .ne. 10) then + if (itype(i,1) .ne. 10) then + ea(1,i) = c(1,i+nres) + ea(2,i) = c(2,i+nres) + ea(3,i) = c(3,i+nres) + else + ea(1,i) = c(1,i) + ea(2,i) = c(2,i) + ea(3,i) = c(3,i) + end if + end do + call IdentityM(resM) + if (nres .le. 2) then + print *, "nres too small (should be at least 2), stopping" + stop + end if + do i=1,3 + v1(i)=ea(i,1) + v2(i)=ea(i,2) + end do +!c ! szukamy najwiekszej odleglosci miedzy atomami efektywnymi ea + call Dist3d(maxd,v1,v2) +!c ! odleglosc miedzy pierwsza para atomow efektywnych + maxi = 1 + maxj = 2 + do i=1,nres-1 + do j=i+1,nres + v1(1)=ea(1,i) + v1(2)=ea(2,i) + v1(3)=ea(3,i) + v2(1)=ea(1,j) + v2(2)=ea(2,j) + v2(3)=ea(3,j) + call Dist3d(dd,v1,v2) + if (dd .gt. maxd) then + maxd = dd + maxi = i + maxj = j + end if + end do + end do + vecnea(1)=ea(1,maxi)-ea(1,maxj) + vecnea(2)=ea(2,maxi)-ea(2,maxj) + vecnea(3)=ea(3,maxi)-ea(3,maxj) + if (vecnea(1) .lt. 0) then + vecnea(1) = -vecnea(1) + vecnea(2) = -vecnea(2) + vecnea(3) = -vecnea(3) + end if +!c ! obliczenie kata obrotu wokol osi Z + fi = -atan2(vecnea(2),vecnea(1)) + call RotateZ(M,fi) +!c ! obliczenie kata obrotu wokol osi Y + fi = atan2(vecnea(3), sqrt(sq(vecnea(1))+sq(vecnea(2)))) + call RotateY(M2,fi) + M = matmul(M2,M) +!c ! Przeksztalcamy wszystkie atomy efektywne +!c ! uzyskujac najwieksza odleglosc ulożona wzdluz OX +!c ! ea = transform_eatoms(ea,M) + do i=1,nres + v1(1)=ea(1,i) + v1(2)=ea(2,i) + v1(3)=ea(3,i) + call tranform_point(v2,v1,M) + ea(1,i)=v2(1) + ea(2,i)=v2(2) + ea(3,i)=v2(3) + end do + resM = M +!c ! Teraz szukamy najdluzszego rzutu na plaszczyzne YZ +!c ! (czyli w liczeniu odleglosci bierzemy pod uwage tylko wsp. y, z) + maxd = sqrt( sq(ea(2,1)-ea(2,2)) + sq(ea(3,1)-ea(3,2))) ! aktualnie max odl + maxi = 1 ! indeksy atomow + maxj = 2 ! miedzy ktorymi jest max odl (chwilowe) + do i=1,nres-1 + do j=i+1,nres + dd = sqrt( (ea(2,i)-ea(2,j))**2 + (ea(3,i)-ea(3,j))**2) + if (dd .gt. maxd) then + maxd = dd + maxi = i + maxj = j + end if + end do + end do +!c ! Teraz obrocimy wszystko wokol OX tak, zeby znaleziony rzut +!c ! byl rownolegly do OY + vecnea(1) = ea(1,maxi)-ea(1,maxj) + vecnea(2) = ea(2,maxi)-ea(2,maxj) + vecnea(3) = ea(3,maxi)-ea(3,maxj) +!c ! jeśli współrzędna vecnea.y < 0, to robimy odwrotnie + if (vecnea(2) .lt. 0) then + vecnea(1) = -vecnea(1) + vecnea(2) = -vecnea(2) + vecnea(3) = -vecnea(3) + end if +!c ! obliczenie kąta obrotu wokół osi X + fi = -atan2(vecnea(3),vecnea(2)) + call RotateX(M,fi) +!c ! Przeksztalcamy wszystkie atomy efektywne + do i=1,nres + v1(1)=ea(1,i) + v1(2)=ea(2,i) + v1(3)=ea(3,i) + call tranform_point(v2,v1,M) + ea(1,i)=v2(1) + ea(2,i)=v2(2) + ea(3,i)=v2(3) + end do + resM = matmul(M,resM) ! zbieramy wynik (sprawdzic kolejnosc M,resM) +!c ! centrujemy + mean_ea(1) = 0 + mean_ea(2) = 0 + mean_ea(3) = 0 + do i=1,nres + mean_ea(1) = mean_ea(1) + ea(1,i) + mean_ea(2) = mean_ea(2) + ea(2,i) + mean_ea(3) = mean_ea(3) + ea(3,i) + end do + v1(1) = -mean_ea(1)/nres + v1(2) = -mean_ea(2)/nres + v1(3) = -mean_ea(3)/nres + call TranslateV(M,v1) + resM = matmul(M,resM) +!c ! przesuwamy + do i=1,nres + ea(1,i) = ea(1,i) + v1(1) + ea(2,i) = ea(2,i) + v1(2) + ea(3,i) = ea(3,i) + v1(3) + end do + res = resM +!c ! wynikowa macierz przeksztalcenia lancucha +!c ! (ale lancuch w ea juz mamy przeksztalcony) + return + end subroutine + double precision function compute_rd + use geometry_data, only: nres + use energy_data, only: itype + implicit none + double precision or_mat(4,4) +! double precision hydrophobicity + integer neatoms + double precision cutoff + double precision ho(70000) + double precision ht(70000) + double precision hosum, htsum + double precision marg, sigmax, sigmay, sigmaz + integer i, j + double precision v1(3) + double precision v2(3) + double precision rijdivc, coll, tmpkwadrat, tmppotega, dist + double precision OdivT, OdivR, ot_one, or_one, RD_classic + call orientation_matrix(or_mat) +!c ! tam juz liczy sie tablica ea + neatoms = nres + cutoff = 8.99d0 +!c ! granica oddzialywania w A (powyzej ignorujemy oddzialywanie) +!c ! Najpierw liczymy "obserwowana hydrofobowosc" + hosum = 0.0d0 ! na sume pol ho, do celow pozniejszej normalizacji + do j=1,neatoms + ho(j)=0.0d0 + do i=1,neatoms + if (j .eq. i) then ! nie uwzgledniamy oddzialywania atomu z samym soba + cycle + end if + v1(1)=ea(1,i) + v1(2)=ea(2,i) + v1(3)=ea(3,i) + v2(1)=ea(1,j) + v2(2)=ea(2,j) + v2(3)=ea(3,j) + call Dist3d(dist,v1,v2) ! odleglosc miedzy atomami + if (dist .gt. cutoff) then ! za daleko, nie uwzgledniamy + cycle + end if + rijdivc = dist / cutoff + coll = 0.0d0 + tmppotega = rijdivc*rijdivc + tmpkwadrat = tmppotega + coll = coll + 7*tmpkwadrat + tmppotega = tmppotega * tmpkwadrat ! do potęgi 4 + coll = coll - 9*tmppotega + tmppotega = tmppotega * tmpkwadrat ! do potęgi 6 + coll = coll + 5*tmppotega + tmppotega = tmppotega * tmpkwadrat ! do potęgi 8 + coll = coll - tmppotega +!c ! Wersja: Bryliński 2007 +!c ! EAtoms[j].collectedhp += EAtoms[i].hyphob*(1 - 0.5 * coll); +!c ! ea$ho[j] = ea$ho[j] + hydrophobicity(ea$resid[i])*(1-0.5*coll) +!c ! Wersja: Banach Konieczny Roterman 2014 +!c ! EAtoms[j].collectedhp += (EAtoms[i].hyphob+EAtoms[j].hyphob)*(1 - 0.5 * coll); +!c ponizej bylo itype(i,1) w miejscu itype(i) oraz itype(j,1) w miejscu itype(j) + ho(j) = ho(j) + (hydrophobicity(itype(i,1))+& + hydrophobicity(itype(j,1)))*(1.0d0-0.5_8*coll) + end do + hosum = hosum + ho(j) + end do +!c ! Normalizujemy + do i=1,neatoms + ho(i) = ho(i) / hosum + end do +!c ! Koniec liczenia hydrofobowosci obserwowanej (profil ho) +!c ! Teraz liczymy "teoretyczna hydrofobowosc", wedlug kropli i rozkladu Gaussa + htsum = 0.0d0 +!c ! tu zbieramy sume ht, uzyjemy potem do normalizacji +!c ! Ustalimy teraz parametry rozkladu Gaussa, czyli sigmy (srodek jest w (0,0,0)). +!c ! To bedzie (max odl od srodka + margines) / 3, oddzielnie dla kazdej wspolrzednej. + marg = 9.0d0 + htsum = 0.0d0 +!c ! jeszcze raz zerujemy +!c ! szukamy ekstremalnej wartosci wspolrzednej x (max wart bezwzgl) + sigmax = ea(1,1) + do i=2,neatoms + if (abs(ea(1,i))>sigmax) then + sigmax = abs(ea(1,i)) + end if + end do + sigmax = (marg + sigmax) / 3.0d0 +!c ! szukamy ekstremalnej wartosci wspolrzednej y (max wart bezwzgl) + sigmay = ea(2,1) + do i=2,neatoms + if (abs(ea(2,i))>sigmay) then + sigmay = abs(ea(2,i)) + end if + end do + sigmay = (marg + sigmay) / 3.0d0 +!c ! szukamy ekstremalnej wartosci wspolrzednej z (max wart bezwzgl) + sigmaz = ea(3,1) + do i=2,neatoms + if (abs(ea(3,i))>sigmaz) then + sigmaz = abs(ea(3,i)) + end if + end do + sigmaz = (marg + sigmaz) / 3.0d0 +!c !sigmax = (marg + max(abs(max(ea$acoor[,1])), abs(min(ea$acoor[,1]))))/3.0 +!c !sigmay = (marg + max(abs(max(ea$acoor[,2])), abs(min(ea$acoor[,2]))))/3.0 +!c !sigmaz = (marg + max(abs(max(ea$acoor[,3])), abs(min(ea$acoor[,3]))))/3.0 +!c ! print *,"sigmax =",sigmax," sigmay =",sigmay," sigmaz = ",sigmaz + do j=1,neatoms + ht(j)= exp(-(ea(1,j))**2/(2*sigmax**2))& + * exp(-(ea(2,j))**2/(2*sigmay**2)) & + * exp(-(ea(3,j))**2/(2*sigmaz**2)) + htsum = htsum + ht(j) + end do +!c ! Normalizujemy + do i=1, neatoms + ht(i) = ht(i) / htsum + end do +!c ! Teraz liczymy RD + OdivT = 0.0d0 + OdivR = 0.0d0 + do j=1,neatoms + if (ho(j) .ne. 0) then + ot_one = ho(j) * log(ho(j)/ht(j)) / log(2.0d0) + OdivT = OdivT + ot_one + or_one = ho(j) * log(ho(j)/ (1.0d0/neatoms)) / log(2.0_8) + OdivR = OdivR + or_one + endif + end do + RD_classic = OdivT / (OdivT+OdivR) + compute_rd = RD_classic + return + end function + function hydrophobicity(id) ! do przepisania (bylo: identyfikowanie aa po nazwach) + integer id + double precision hydrophobicity + hydrophobicity = 0.0d0 + if (id .eq. 1) then + hydrophobicity = 1.000d0 ! CYS + return + endif + if (id .eq. 2) then + hydrophobicity = 0.828d0 ! MET + return + endif + if (id .eq. 3) then + hydrophobicity = 0.906d0 ! PHE + return + endif + if (id .eq. 4) then + hydrophobicity = 0.883d0 ! ILE + return + endif + if (id .eq. 5) then + hydrophobicity = 0.783d0 ! LEU + return + endif + if (id .eq. 6) then + hydrophobicity = 0.811d0 ! VAL + return + endif + if (id .eq. 7) then + hydrophobicity = 0.856d0 ! TRP + return + endif + if (id .eq. 8) then + hydrophobicity = 0.700d0 ! TYR + return + endif + if (id .eq. 9) then + hydrophobicity = 0.572d0 ! ALA + return + endif + if (id .eq. 10) then + hydrophobicity = 0.550d0 ! GLY + return + endif + if (id .eq. 11) then + hydrophobicity = 0.478d0 ! THR + return + endif + if (id .eq. 12) then + hydrophobicity = 0.422d0 ! SER + return + endif + if (id .eq. 13) then + hydrophobicity = 0.250d0 ! GLN + return + endif + if (id .eq. 14) then + hydrophobicity = 0.278d0 ! ASN + return + endif + if (id .eq. 15) then + hydrophobicity = 0.083d0 ! GLU + return + endif + if (id .eq. 16) then + hydrophobicity = 0.167d0 ! ASP + return + endif + if (id .eq. 17) then + hydrophobicity = 0.628d0 ! HIS + return + endif + if (id .eq. 18) then + hydrophobicity = 0.272d0 ! ARG + return + endif + if (id .eq. 19) then + hydrophobicity = 0.000d0 ! LYS + return + endif + if (id .eq. 20) then + hydrophobicity = 0.300d0 ! PRO + return + endif + return + end function hydrophobicity + subroutine mycrossprod(res,b,c) + implicit none + double precision, intent(out) :: res(3) + double precision, intent(in) :: b(3) + double precision, intent(in) :: c(3) +!c ! Tylko dla wektorów trójwymiarowych, ale nie sprawdzamy tego tutaj + res(1) = b(2)*c(3)-b(3)*c(2) + res(2) = b(3)*c(1)-b(1)*c(3) + res(3) = b(1)*c(2)-b(2)*c(1) + return + end subroutine + subroutine mydotprod(res,b,c) + implicit none + double precision, intent(out) :: res + double precision, intent(in) :: b(3) + double precision, intent(in) :: c(3) +!c ! Tylko dla wektorów trójwymiarowych, ale nie sprawdzamy tego tutaj + res = b(1)*c(1)+b(2)*c(2)+b(3)*c(3) + return + end subroutine +!c ! cosinus k¹ta miêdzy wektorami trójwymiarowymi + subroutine cosfi(res, x, y) + implicit none + double precision, intent(out) :: res + double precision, intent(in) :: x(3) + double precision, intent(in) :: y(3) + double precision LxLy + LxLy=sqrt(x(1)*x(1)+x(2)*x(2)+x(3)*x(3)) *& + sqrt(y(1)*y(1)+y(2)*y(2)+y(3)*y(3)) + if (LxLy==0.0) then + res = 0.0d0 + else + call mydotprod(res,x,y) + res = res / LxLy + end if + return + end subroutine + + + subroutine Dist3d(res,v1,v2) + implicit none + double precision, intent(out) :: res + double precision, intent(in) :: v1(3) + double precision, intent(in) :: v2(3) +! double precision sq + res = sqrt( sq(v1(1)-v2(1)) + sq(v1(2)-v2(2)) + sq(v1(3)-v2(3))) + return + end subroutine +!c ! Przeksztalca wsp. 3d uzywajac macierzy przeksztalcenia M (4x4) + subroutine tranform_point(res,v3d,M) + implicit none + double precision, intent(out) :: res(3) + double precision, intent(in) :: v3d(3) + double precision, intent(in) :: M(4,4) + + res(1) = M(1,1)*v3d(1) + M(1,2)*v3d(2) + M(1,3)*v3d(3) + M(1,4) + res(2) = M(2,1)*v3d(1) + M(2,2)*v3d(2) + M(2,3)*v3d(3) + M(2,4) + res(3) = M(3,1)*v3d(1) + M(3,2)*v3d(2) + M(3,3)*v3d(3) + M(3,4) + return + end subroutine +!c ! TranslateV: macierz translacji o wektor V + subroutine TranslateV(res,V) + implicit none + double precision, intent(out) :: res(4,4) + double precision, intent(in) :: v(3) + res(1,1) = 1.0d0 + res(1,2) = 0 + res(1,3) = 0 + res(1,4) = v(1) + res(2,1) = 0 + res(2,2) = 1.0d0 + res(2,3) = 0 + res(2,4) = v(2) + res(3,1) = 0 + res(3,2) = 0 + res(3,3) = 1.0d0 + res(3,4) = v(3) + res(4,1) = 0 + res(4,2) = 0 + res(4,3) = 0 + res(4,4) = 1.0d0 + return + end subroutine +!c ! RotateX: macierz obrotu wokol osi OX o kat fi + subroutine RotateX(res,fi) + implicit none + double precision, intent(out) :: res(4,4) + double precision, intent(in) :: fi + res(1,1) = 1.0d0 + res(1,2) = 0 + res(1,3) = 0 + res(1,4) = 0 + res(2,1) = 0 + res(2,2) = cos(fi) + res(2,3) = -sin(fi) + res(2,4) = 0 + res(3,1) = 0 + res(3,2) = sin(fi) + res(3,3) = cos(fi) + res(3,4) = 0 + res(4,1) = 0 + res(4,2) = 0 + res(4,3) = 0 + res(4,4) = 1.0d0 + return + end subroutine +!c ! RotateY: macierz obrotu wokol osi OY o kat fi + subroutine RotateY(res,fi) + implicit none + double precision, intent(out) :: res(4,4) + double precision, intent(in) :: fi + res(1,1) = cos(fi) + res(1,2) = 0 + res(1,3) = sin(fi) + res(1,4) = 0 + res(2,1) = 0 + res(2,2) = 1.0d0 + res(2,3) = 0 + res(2,4) = 0 + res(3,1) = -sin(fi) + res(3,2) = 0 + res(3,3) = cos(fi) + res(3,4) = 0 + res(4,1) = 0 + res(4,2) = 0 + res(4,3) = 0 + res(4,4) = 1.0d0 + return + end subroutine +!c ! RotateZ: macierz obrotu wokol osi OZ o kat fi + subroutine RotateZ(res,fi) + implicit none + double precision, intent(out) :: res(4,4) + double precision, intent(in) :: fi + res(1,1) = cos(fi) + res(1,2) = -sin(fi) + res(1,3) = 0 + res(1,4) = 0 + res(2,1) = sin(fi) + res(2,2) = cos(fi) + res(2,3) = 0 + res(2,4) = 0 + res(3,1) = 0 + res(3,2) = 0 + res(3,3) = 1.0d0 + res(3,4) = 0 + res(4,1) = 0 + res(4,2) = 0 + res(4,3) = 0 + res(4,4) = 1.0d0 + return + end subroutine +!c ! IdentityM + subroutine IdentityM(res) + implicit none + double precision, intent(out) :: res(4,4) + res(1,1) = 1.0d0 + res(1,2) = 0 + res(1,3) = 0 + res(1,4) = 0 + res(2,1) = 0 + res(2,2) = 1.0d0 + res(2,3) = 0 + res(2,4) = 0 + res(3,1) = 0 + res(3,2) = 0 + res(3,3) = 1.0d0 + res(3,4) = 0 + res(4,1) = 0 + res(4,2) = 0 + res(4,3) = 0 + res(4,4) = 1.0d0 + return + end subroutine + double precision function sq(x) + double precision x + sq = x*x + return + end function sq + +#ifdef LBFGS + double precision function funcgrad(x,g) + use MD_data, only: totT,usampl + implicit none + double precision energia(0:n_ene) + double precision x(nvar),g(nvar) + integer i + call var_to_geom(nvar,x) + call zerograd + call chainbuild + call etotal(energia(0)) + call sum_gradient + funcgrad=energia(0) + call cart2intgrad(nvar,g) + if (usampl) then + do i=1,nres-3 + gloc(i,icg)=gloc(i,icg)+dugamma(i) + enddo + do i=1,nres-2 + gloc(nphi+i,icg)=gloc(nphi+i,icg)+dutheta(i) + enddo + endif + do i=1,nvar + g(i)=g(i)+gloc(i,icg) + enddo + return + end function funcgrad + subroutine cart2intgrad(n,g) + integer n + double precision g(n) + double precision drt(3,3,nres),rdt(3,3,nres),dp(3,3),& + temp(3,3),prordt(3,3,nres),prodrt(3,3,nres) + double precision xx(3),xx1(3),alphi,omegi,xj,dpjk,yp,xp,xxp,yyp + double precision cosalphi,sinalphi,cosomegi,sinomegi,theta2,& + cost2,sint2,rj,dxoiij,tempkl,dxoijk,dsci,zzp,dj,dpkl + double precision fromto(3,3),aux(6) + integer i,ii,j,jjj,k,l,m,indi,ind,ind1 + logical sideonly + sideonly=.false. + g=0.0d0 + if (sideonly) goto 10 + do i=1,nres-2 + rdt(1,1,i)=-rt(1,2,i) + rdt(1,2,i)= rt(1,1,i) + rdt(1,3,i)= 0.0d0 + rdt(2,1,i)=-rt(2,2,i) + rdt(2,2,i)= rt(2,1,i) + rdt(2,3,i)= 0.0d0 + rdt(3,1,i)=-rt(3,2,i) + rdt(3,2,i)= rt(3,1,i) + rdt(3,3,i)= 0.0d0 + enddo + do i=2,nres-2 + drt(1,1,i)= 0.0d0 + drt(1,2,i)= 0.0d0 + drt(1,3,i)= 0.0d0 + drt(2,1,i)= rt(3,1,i) + drt(2,2,i)= rt(3,2,i) + drt(2,3,i)= rt(3,3,i) + drt(3,1,i)=-rt(2,1,i) + drt(3,2,i)=-rt(2,2,i) + drt(3,3,i)=-rt(2,3,i) + enddo + ind1=0 + do i=1,nres-2 + ind1=ind1+1 + if (n.gt.nphi) then + + do j=1,3 + do k=1,2 + dpjk=0.0D0 + do l=1,3 + dpjk=dpjk+prod(j,l,i)*rdt(l,k,i) + enddo + dp(j,k)=dpjk + prordt(j,k,i)=dp(j,k) + enddo + dp(j,3)=0.0D0 + g(nphi+i)=g(nphi+i)+vbld(i+2)*dp(j,1)*gradc(j,i+1,icg) + enddo + xx1(1)=-0.5D0*xloc(2,i+1) + xx1(2)= 0.5D0*xloc(1,i+1) + do j=1,3 + xj=0.0D0 + do k=1,2 + xj=xj+r(j,k,i)*xx1(k) + enddo + xx(j)=xj + enddo + do j=1,3 + rj=0.0D0 + do k=1,3 + rj=rj+prod(j,k,i)*xx(k) + enddo + g(nphi+i)=g(nphi+i)+rj*gradx(j,i+1,icg) + enddo + if (i.lt.nres-2) then + do j=1,3 + dxoiij=0.0D0 + do k=1,3 + dxoiij=dxoiij+dp(j,k)*xrot(k,i+2) + enddo + g(nphi+i)=g(nphi+i)+dxoiij*gradx(j,i+2,icg) + enddo + endif + + endif + + + if (i.gt.1) then + do j=1,3 + do k=1,3 + dpjk=0.0 + do l=2,3 + dpjk=dpjk+prod(j,l,i)*drt(l,k,i) + enddo + dp(j,k)=dpjk + prodrt(j,k,i)=dp(j,k) + enddo + g(i-1)=g(i-1)+vbld(i+2)*dp(j,1)*gradc(j,i+1,icg) + enddo + endif + xx(1)= 0.0D0 + xx(3)= xloc(2,i+1)*r(2,2,i)+xloc(3,i+1)*r(2,3,i) + xx(2)=-xloc(2,i+1)*r(3,2,i)-xloc(3,i+1)*r(3,3,i) + if (i.gt.1) then + do j=1,3 + rj=0.0D0 + do k=2,3 + rj=rj+prod(j,k,i)*xx(k) + enddo + g(i-1)=g(i-1)-rj*gradx(j,i+1,icg) + enddo + endif + if (i.gt.1) then + do j=1,3 + dxoiij=0.0D0 + do k=1,3 + dxoiij=dxoiij+dp(j,k)*xrot(k,i+2) + enddo + g(i-1)=g(i-1)+dxoiij*gradx(j,i+2,icg) + enddo + endif + do j=i+1,nres-2 + ind1=ind1+1 + call build_fromto(i+1,j+1,fromto) + do k=1,3 + do l=1,3 + tempkl=0.0D0 + do m=1,2 + tempkl=tempkl+prordt(k,m,i)*fromto(m,l) + enddo + temp(k,l)=tempkl + enddo + enddo + if (n.gt.nphi) then + do k=1,3 + g(nphi+i)=g(nphi+i)+vbld(j+2)*temp(k,1)*gradc(k,j+1,icg) + enddo + do k=1,3 + dxoijk=0.0D0 + do l=1,3 + dxoijk=dxoijk+temp(k,l)*xrot(l,j+2) + enddo + g(nphi+i)=g(nphi+i)+dxoijk*gradx(k,j+2,icg) + enddo + endif + do k=1,3 + do l=1,3 + tempkl=0.0D0 + do m=1,3 + tempkl=tempkl+prodrt(k,m,i)*fromto(m,l) + enddo + temp(k,l)=tempkl + enddo + enddo + if (i.gt.1) then + do k=1,3 + g(i-1)=g(i-1)+vbld(j+2)*temp(k,1)*gradc(k,j+1,icg) + enddo + do k=1,3 + dxoijk=0.0D0 + do l=1,3 + dxoijk=dxoijk+temp(k,l)*xrot(l,j+2) + enddo + g(i-1)=g(i-1)+dxoijk*gradx(k,j+2,icg) + enddo + endif + enddo + enddo + + if (nvar.le.nphi+ntheta) return + + 10 continue + do i=2,nres-1 + if (iabs(itype(i,1)).eq.10 .or. itype(i,1).eq.ntyp1& !) cycle + .or. mask_side(i).eq.0 ) cycle + ii=ialph(i,1) + dsci=vbld(i+nres) +#ifdef OSF + alphi=alph(i) + omegi=omeg(i) + if(alphi.ne.alphi) alphi=100.0 + if(omegi.ne.omegi) omegi=-100.0 +#else + alphi=alph(i) + omegi=omeg(i) +#endif + 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 + 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) + enddo + aux(jjj+k)=dj + enddo + jjj=jjj+3 + enddo + do k=1,3 + g(ii)=g(ii)+aux(k)*gradx(k,i,icg) + g(ii+nside)=g(ii+nside)+aux(k+3)*gradx(k,i,icg) + enddo + enddo + return + end subroutine cart2intgrad + + +#endif + +!-----------LIPID-MARTINI-UNRES-PROTEIN + +! new for K+ + subroutine elip_prot(evdw) +! subroutine emart_prot2(emartion_prot) + use calc_data + use comm_momo + + logical :: lprn +!el local variables + integer :: iint,itypi1,subchap,isel,itmp + real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi + real(kind=8) :: evdw,aa,bb + real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,& + dist_temp, dist_init,ssgradlipi,ssgradlipj, & + sslipi,sslipj,faclip,alpha_sco + integer :: ii,ki + real(kind=8) :: fracinbuf + real (kind=8) :: escpho + real (kind=8),dimension(4):: ener + real(kind=8) :: b1,b2,egb + real(kind=8) :: Fisocav,ECL,Elj,Equad,Epol,eheadtail,& + Lambf,& + Chif,ChiLambf,Fcav,dFdR,dFdOM1,& + emartions_prot_amber,dFdOM2,dFdL,dFdOM12,& + federmaus,& + d1i,d1j +! real(kind=8),dimension(3,2)::erhead_tail +! real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead,Rtail_distance + real(kind=8) :: facd4, adler, Fgb, facd3 + integer troll,jj,istate + real (kind=8) :: dcosom1(3),dcosom2(3) + real(kind=8) ::locbox(3) + locbox(1)=boxxsize + locbox(2)=boxysize + locbox(3)=boxzsize + + evdw=0.0D0 + if (nres_molec(4).eq.0) return + eps_out=80.0d0 +! sss_ele_cut=1.0d0 + + itmp=0 + do i=1,4 + itmp=itmp+nres_molec(i) + enddo +! go to 17 +! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization +! do i=ibond_start,ibond_end + do ki=g_listmartsc_start,g_listmartsc_end + i=newcontlistmartsci(ki) + j=newcontlistmartscj(ki) + +! print *,"I am in EVDW",i + itypi=iabs(itype(i,1)) + +! if (i.ne.47) cycle + if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle + itypi1=iabs(itype(i+1,1)) + xi=c(1,nres+i) + yi=c(2,nres+i) + zi=c(3,nres+i) + call to_box(xi,yi,zi) + call lipid_layer(xi,yi,zi,sslipi,ssgradlipi) + dxi=dc_norm(1,nres+i) + dyi=dc_norm(2,nres+i) + dzi=dc_norm(3,nres+i) + dsci_inv=vbld_inv(i+nres) +! do j=itmp+1,itmp+nres_molec(5) + +! Calculate SC interaction energy. + itypj=iabs(itype(j,4)) + if ((itypj.gt.ntyp_molec(4))) cycle + CALL elgrad_init_mart(eheadtail,Egb,Ecl,Elj,Equad,Epol) +! print *,i,j,"after elgrad" + dscj_inv=0.0 + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + + call to_box(xj,yj,zj) +! write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,xj,yj,zj + +! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj) +! aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 & +! +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 +! bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 & +! +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0 + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) +! write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize + rreal(1)=xj + rreal(2)=yj + rreal(3)=zj + dxj=0.0 + dyj=0.0 + dzj=0.0 +! dxj = dc_norm( 1, nres+j ) +! dyj = dc_norm( 2, nres+j ) +! dzj = dc_norm( 3, nres+j ) + + itypi = itype(i,1) + itypj = itype(j,4) +! Parameters from fitting the analitical expressions to the PMF obtained by umbrella +! sampling performed with amber package +! alf1 = 0.0d0 +! alf2 = 0.0d0 +! alf12 = 0.0d0 +! a12sq = rborn(itypi,itypj) * rborn(itypj,itypi) + chi1 = chi1mart(itypi,itypj) + chis1 = chis1mart(itypi,itypj) + chip1 = chipp1mart(itypi,itypj) +! chi1=0.0d0 +! chis1=0.0d0 +! chip1=0.0d0 + chi2=0.0 + chip2=0.0 + chis2=0.0 +! chis2 = chis(itypj,itypi) + chis12 = chis1 * chis2 + sig1 = sigmap1mart(itypi,itypj) + sig2=0.0d0 +! sig2 = sigmap2(itypi,itypj) +! alpha factors from Fcav/Gcav + b1cav = alphasurmart(1,itypi,itypj) + b2cav = alphasurmart(2,itypi,itypj) + b3cav = alphasurmart(3,itypi,itypj) + b4cav = alphasurmart(4,itypi,itypj) + +! b1cav=0.0d0 +! b2cav=0.0d0 +! b3cav=0.0d0 +! b4cav=0.0d0 + +! used to determine whether we want to do quadrupole calculations + eps_in = epsintabmart(itypi,itypj) + if (eps_in.eq.0.0) eps_in=1.0 + + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +! Rtail = 0.0d0 + + DO k = 1, 3 + ctail(k,1)=c(k,i+nres) + ctail(k,2)=c(k,j) + END DO + call to_box(ctail(1,1),ctail(2,1),ctail(3,1)) + call to_box(ctail(1,2),ctail(2,2),ctail(3,2)) +!c! tail distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + do k=1,3 + Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k)) + enddo + Rtail = dsqrt( & + (Rtail_distance(1)*Rtail_distance(1)) & + + (Rtail_distance(2)*Rtail_distance(2)) & + + (Rtail_distance(3)*Rtail_distance(3))) +! tail lomartion and distance calculations +! dhead1 + d1 = dheadmart(1, 1, itypi, itypj) +! d2 = dhead(2, 1, itypi, itypj) + DO k = 1,3 +! lomartion of polar head is computed by taking hydrophobic centre +! and moving by a d1 * dc_norm vector +! see unres publimartions for very informative images + chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) + chead(k,2) = c(k, j) + enddo + call to_box(chead(1,1),chead(2,1),chead(3,1)) + call to_box(chead(1,2),chead(2,2),chead(3,2)) +! write(iout,*) "TEST",chead(1,1),chead(2,1),chead(3,1),dc_norm(k, i+nres),d1 +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + do k=1,3 + Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k)) + 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 + Fisocav=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) + sss_ele_cut=sscale_ele(1.0d0/(rij)) + sss_ele_grad=sscagrad_ele(1.0d0/(rij)) +! print *,sss_ele_cut,sss_ele_grad,& +! 1.0d0/(rij),r_cut_ele,rlamb_ele + if (sss_ele_cut.le.0.0) cycle + 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 = Rtail - sig + sig0ij + IF (rij_shift.le.0.0D0) THEN + evdw = 1.0D20 + if (evdw.gt.1.0d6) then + write (*,'(2(1x,a3,i3),7f7.2)') & + restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& + 1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij,sigsq + write(*,*) facsig,faceps1_inv,om1,chiom1,chi1 + write(*,*) "ANISO?!",chi1 +!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& +! Equad,evdwij+Fcav+eheadtail,evdw + endif + + RETURN + END IF + sigder = -sig * sigsq + rij_shift = 1.0D0 / rij_shift + fac = rij_shift**expon + c1 = fac * fac * aa_aq_mart(itypi,itypj) +! print *,"ADAM",aa_aq(itypi,itypj) + +! c1 = 0.0d0 + c2 = fac * bb_aq_mart(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 +!#ifdef TSCSC +! IF (bb_aq(itypi,itypj).gt.0) THEN +! evdw_p = evdw_p + evdwij +! ELSE +! evdw_m = evdw_m + evdwij +! END IF +!#else + evdw = evdw & + + evdwij*sss_ele_cut +!#endif + c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 + fac = -expon * (c1 + evdwij) * rij_shift + sigder = fac * sigder +! Calculate distance derivative + gg(1) = fac +!*sss_ele_cut+evdwij*sss_ele_grad + gg(2) = fac +!*sss_ele_cut+evdwij*sss_ele_grad + gg(3) = fac +!*sss_ele_cut+evdwij*sss_ele_grad +! print *,"GG(1),distance grad",gg(1) + fac = chis1 * sqom1 + chis2 * sqom2 & + - 2.0d0 * chis12 * om1 * om2 * om12 + pom = 1.0d0 - chis1 * chis2 * sqom12 + Lambf = (1.0d0 - (fac / pom)) + Lambf = dsqrt(Lambf) + sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0) + Chif = Rtail * sparrow + ChiLambf = Chif * Lambf + eagle = dsqrt(ChiLambf) + bat = ChiLambf ** 11.0d0 + top = b1cav * ( eagle + b2cav * ChiLambf - b3cav ) + bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0) + botsq = bot * bot + Fcav = top / bot + + dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf)) + dbot = 12.0d0 * b4cav * bat * Lambf + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow + dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif)) + dbot = 12.0d0 * b4cav * 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) + dCAVdOM1 = dFdL * ( dFdOM1 ) + dCAVdOM2 = dFdL * ( dFdOM2 ) + dCAVdOM12 = dFdL * ( dFdOM12 ) + + DO k= 1, 3 + ertail(k) = Rtail_distance(k)/Rtail + END DO + erdxi = scalar( ertail(1), dC_norm(1,i+nres) ) + erdxj = scalar( ertail(1), dC_norm(1,j) ) + facd1 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres) + facd2 = dtailmart(2,itypi,itypj) * vbld_inv(j) + DO k = 1, 3 + pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres)) + gradpepmartx(k,i) = gradpepmartx(k,i) & + - (( dFdR + gg(k) ) * pom)*sss_ele_cut& + -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k) + + pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j)) +! gvdwx(k,j) = gvdwx(k,j) & +! + (( dFdR + gg(k) ) * pom) + gradpepmart(k,i) = gradpepmart(k,i) & + - (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut& + -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k) + + gradpepmart(k,j) = gradpepmart(k,j) & + + (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut& + +(evdwij+Fcav)*rij*sss_ele_grad*rreal(k) + + gg(k) = 0.0d0 + ENDDO +!c! Compute head-head and head-tail energies for each state +!! if (.false.) then ! turn off electrostatic + isel = iabs(Qi)+iabs(Qj) + if ((itype(j,4).gt.4).and.(itype(j,4).lt.14)) isel=isel+2 +! isel=0 +! if (isel.eq.2) isel=0 + IF (isel.le.1) THEN + eheadtail = 0.0d0 + ELSE IF (isel.eq.3) THEN + if (iabs(Qj).eq.1) then + CALL edq_mart(ecl, elj, epol) + eheadtail = ECL + elj + epol + else + if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then + Qi=Qi*2 + Qij=Qij*2 + endif + call eqd_mart(ecl,elj,epol) + eheadtail = ECL + elj + epol + endif + ELSE IF ((isel.eq.2)) THEN + if (iabs(Qi).ne.1) then + eheadtail=0.0d0 + else + if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then + Qi=Qi*2 + Qij=Qij*2 + endif + CALL eqq_mart(Ecl,Egb,Epol,Fisocav,Elj) + eheadtail = ECL + Egb + Epol + Fisocav + Elj + endif + ELSE IF (isel.eq.4) then + call edd_mart(ecl) + eheadtail = ECL + ENDIF +! write(iout,*) "not yet implemented",j,itype(j,5) +!! endif ! turn off electrostatic + evdw = evdw + (Fcav + eheadtail)*sss_ele_cut +! if (evdw.gt.1.0d6) then +! write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') & +! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& +! 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& +! Equad,evdwij+Fcav+eheadtail,evdw +! endif + + IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') & + restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& + 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& + Equad,evdwij+Fcav+eheadtail,evdw +! evdw = evdw + Fcav + eheadtail + if (energy_dec) write(iout,*) "FCAV", & + sig1,sig2,b1cav,b2cav,b3cav,b4cav +! print *,"before sc_grad_mart", i,j, gradpepmart(1,j) +! iF (nstate(itypi,itypj).eq.1) THEN + CALL sc_grad_mart +! print *,"after sc_grad_mart", i,j, gradpepmart(1,j) + +! END IF +!c!------------------------------------------------------------------- +!c! NAPISY KONCOWE + END DO ! j +! END DO ! i +!c write (iout,*) "Number of loop steps in EGB:",ind +!c energy_dec=.false. +! print *,"EVDW KURW",evdw,nres +!!! return + 17 continue +! go to 23 +! do i=ibond_start,ibond_end + + do ki=g_listmartp_start,g_listmartp_end + i=newcontlistmartpi(ki) + j=newcontlistmartpj(ki) + +! print *,"I am in EVDW",i + itypi=10 ! the peptide group parameters are for glicine + +! if (i.ne.47) cycle + if ((itype(i,1).eq.ntyp1).or.itype(i+1,1).eq.ntyp1) cycle + itypi1=iabs(itype(i+1,1)) + 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 + call to_box(xi,yi,zi) + dxi=dc_norm(1,i) + dyi=dc_norm(2,i) + dzi=dc_norm(3,i) + dsci_inv=vbld_inv(i+1)/2.0 +! do j=itmp+1,itmp+nres_molec(5) + +! Calculate SC interaction energy. + itypj=iabs(itype(j,4)) + if ((itypj.gt.ntyp_molec(4))) cycle + CALL elgrad_init_mart_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol) + + dscj_inv=0.0 + xj=c(1,j) + yj=c(2,j) + zj=c(3,j) + call to_box(xj,yj,zj) + xj=boxshift(xj-xi,boxxsize) + yj=boxshift(yj-yi,boxysize) + zj=boxshift(zj-zi,boxzsize) + rreal(1)=xj + rreal(2)=yj + rreal(3)=zj + + dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2 + + dxj = 0.0d0! dc_norm( 1, nres+j ) + dyj = 0.0d0!dc_norm( 2, nres+j ) + dzj = 0.0d0! dc_norm( 3, nres+j ) + + itypi = 10 + itypj = itype(j,4) +! Parameters from fitting the analitical expressions to the PMF obtained by umbrella +! sampling performed with amber package +! alf1 = 0.0d0 +! alf2 = 0.0d0 +! alf12 = 0.0d0 +! a12sq = rborn(itypi,itypj) * rborn(itypj,itypi) + chi1 = chi1mart(itypi,itypj) + chis1 = chis1mart(itypi,itypj) + chip1 = chipp1mart(itypi,itypj) +! chi1=0.0d0 +! chis1=0.0d0 +! chip1=0.0d0 + chi2=0.0 + chip2=0.0 + chis2=0.0 +! chis2 = chis(itypj,itypi) + chis12 = chis1 * chis2 + sig1 = sigmap1mart(itypi,itypj) + sig2=0.0 +! sig2 = sigmap2(itypi,itypj) +! alpha factors from Fcav/Gcav + b1cav = alphasurmart(1,itypi,itypj) + b2cav = alphasurmart(2,itypi,itypj) + b3cav = alphasurmart(3,itypi,itypj) + b4cav = alphasurmart(4,itypi,itypj) + +! used to determine whether we want to do quadrupole calculations + eps_in = epsintabmart(itypi,itypj) + if (eps_in.eq.0.0) eps_in=1.0 + + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +! Rtail = 0.0d0 + + DO k = 1, 3 + ctail(k,1)=(c(k,i)+c(k,i+1))/2.0 + ctail(k,2)=c(k,j) + END DO + call to_box(ctail(1,1),ctail(2,1),ctail(3,1)) + call to_box(ctail(1,2),ctail(2,2),ctail(3,2)) +!c! tail distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + do k=1,3 + Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k)) + enddo + +!c! tail distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + Rtail = dsqrt( & + (Rtail_distance(1)*Rtail_distance(1)) & + + (Rtail_distance(2)*Rtail_distance(2)) & + + (Rtail_distance(3)*Rtail_distance(3))) +! tail lomartion and distance calculations +! dhead1 + d1 = dheadmart(1, 1, itypi, itypj) +! print *,"d1",d1 +! d1=0.0d0 +! d2 = dhead(2, 1, itypi, itypj) + DO k = 1,3 +! lomartion of polar head is computed by taking hydrophobic centre +! and moving by a d1 * dc_norm vector +! see unres publimartions for very informative images + chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i) + chead(k,2) = c(k, j) + ENDDO +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + call to_box(chead(1,1),chead(2,1),chead(3,1)) + call to_box(chead(1,2),chead(2,2),chead(3,2)) + +! distance +! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + do k=1,3 + Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k)) + 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 = 0.0d0 ! 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) + sss_ele_cut=sscale_ele(1.0d0/(rij)) + sss_ele_grad=sscagrad_ele(1.0d0/(rij)) +! print *,sss_ele_cut,sss_ele_grad,& +! 1.0d0/(rij),r_cut_ele,rlamb_ele + if (sss_ele_cut.le.0.0) cycle + 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 + om2=0.0d0 + om12=0.0d0 + 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 = Rtail - sig + sig0ij + IF (rij_shift.le.0.0D0) THEN + evdw = 1.0D20 +! if (evdw.gt.1.0d6) then +! write (*,'(2(1x,a3,i3),6f6.2)') & +! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& +! 1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij +!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& +! Equad,evdwij+Fcav+eheadtail,evdw +! endif + RETURN + END IF + sigder = -sig * sigsq + rij_shift = 1.0D0 / rij_shift + fac = rij_shift**expon + c1 = fac * fac * aa_aq_mart(itypi,itypj) +! print *,"ADAM",aa_aq(itypi,itypj) + +! c1 = 0.0d0 + c2 = fac * bb_aq_mart(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 +!#ifdef TSCSC +! IF (bb_aq(itypi,itypj).gt.0) THEN +! evdw_p = evdw_p + evdwij +! ELSE +! evdw_m = evdw_m + evdwij +! END IF +!#else + evdw = evdw & + + evdwij*sss_ele_cut +!#endif + c1 = c1 * eps1 * eps2rt**2 * eps3rt**2 + fac = -expon * (c1 + evdwij) * rij_shift + sigder = fac * sigder +! Calculate distance derivative + gg(1) = fac + gg(2) = fac + gg(3) = fac + + fac = chis1 * sqom1 + chis2 * sqom2 & + - 2.0d0 * chis12 * om1 * om2 * om12 + + pom = 1.0d0 - chis1 * chis2 * sqom12 +! print *,"TUT2",fac,chis1,sqom1,pom + Lambf = (1.0d0 - (fac / pom)) + Lambf = dsqrt(Lambf) + sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0) + Chif = Rtail * sparrow + ChiLambf = Chif * Lambf + eagle = dsqrt(ChiLambf) + bat = ChiLambf ** 11.0d0 + top = b1cav * ( eagle + b2cav * ChiLambf - b3cav ) + bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0) + botsq = bot * bot + Fcav = top / bot + + dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf)) + dbot = 12.0d0 * b4cav * bat * Lambf + dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow + dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif)) + dbot = 12.0d0 * b4cav * 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) + dCAVdOM1 = dFdL * ( dFdOM1 ) +! dCAVdOM2 = dFdL * ( dFdOM2 ) +! dCAVdOM12 = dFdL * ( dFdOM12 ) + dCAVdOM2=0.0d0 + dCAVdOM12=0.0d0 + + DO k= 1, 3 + ertail(k) = Rtail_distance(k)/Rtail + END DO + erdxi = scalar( ertail(1), dC_norm(1,i) ) + erdxj = scalar( ertail(1), dC_norm(1,j) ) + facd1 = dtailmart(1,itypi,itypj) * vbld_inv(i) + facd2 = dtailmart(2,itypi,itypj) * vbld_inv(j+nres) + DO k = 1, 3 + pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i)) +! gradpepmartx(k,i) = gradpepmartx(k,i) & +! - (( dFdR + gg(k) ) * pom) + pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres)) +! gvdwx(k,j) = gvdwx(k,j) & +! + (( dFdR + gg(k) ) * pom) + gradpepmart(k,i) = gradpepmart(k,i) & + - (( dFdR + gg(k) ) * ertail(k))/2.0d0*sss_ele_cut& + -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)*0.5d0 + gradpepmart(k,i+1) = gradpepmart(k,i+1) & + - (( dFdR + gg(k) ) * ertail(k))/2.0d0*sss_ele_cut& + -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)*0.5d0 + + gradpepmart(k,j) = gradpepmart(k,j) & + + (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut& + +(evdwij+Fcav)*rij*sss_ele_grad*rreal(k) + + gg(k) = 0.0d0 + ENDDO +!c! Compute head-head and head-tail energies for each state +!c! Dipole-charge interactions + isel = 2+iabs(Qj) + if ((itype(j,4).gt.4).and.(itype(j,4).lt.14)) isel=isel+2 +! if (isel.eq.4) isel=0 + if (isel.le.2) then + eheadtail=0.0d0 + ELSE if (isel.eq.3) then + CALL edq_mart_pep(ecl, elj, epol) + eheadtail = ECL + elj + epol +! print *,"i,",i,eheadtail +! eheadtail = 0.0d0 + else +!HERE WATER and other types of molecules solvents will be added +! write(iout,*) "not yet implemented" + CALL edd_mart_pep(ecl) + eheadtail=ecl +! CALL edd_mart_pep +! eheadtail=0.0d0 + endif + evdw = evdw +( Fcav + eheadtail)*sss_ele_cut +! if (evdw.gt.1.0d6) then +! write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') & +! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& +! 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& +! Equad,evdwij+Fcav+eheadtail,evdw +! endif + IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') & + restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,& + 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,& + Equad,evdwij+Fcav+eheadtail,evdw +! evdw = evdw + Fcav + eheadtail + +! iF (nstate(itypi,itypj).eq.1) THEN + CALL sc_grad_mart_pep +! END IF +!c!------------------------------------------------------------------- +!c! NAPISY KONCOWE + END DO ! j +! END DO ! i +!c write (iout,*) "Number of loop steps in EGB:",ind +!c energy_dec=.false. +! print *,"EVDW KURW",evdw,nres + 23 continue +! print *,"before leave sc_grad_mart", i,j, gradpepmart(1,nres-1) + + return + end subroutine elip_prot + + SUBROUTINE eqq_mart(Ecl,Egb,Epol,Fisocav,Elj) + use calc_data + use comm_momo + real (kind=8) :: facd3, facd4, federmaus, adler,& + Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap +! integer :: k +!c! Epol and Gpol analytical parameters + alphapol1 = alphapolmart(itypi,itypj) + alphapol2 = alphapolmart2(itypj,itypi) +!c! Fisocav and Gisocav analytical parameters + al1 = alphisomart(1,itypi,itypj) + al2 = alphisomart(2,itypi,itypj) + al3 = alphisomart(3,itypi,itypj) + al4 = alphisomart(4,itypi,itypj) + csig = (1.0d0 & + / dsqrt(sigiso1mart(itypi, itypj)**2.0d0 & + + sigiso2mart(itypi,itypj)**2.0d0)) +!c! + pis = sig0headmart(itypi,itypj) + eps_head = epsheadmart(itypi,itypj) + Rhead_sq = Rhead * Rhead +!c! R1 - distance between head of ith side chain and tail of jth sidechain +!c! R2 - distance between head of jth side chain and tail of ith sidechain + R1 = 0.0d0 + R2 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances needed by Epol + R1=R1+(ctail(k,2)-chead(k,1))**2 + R2=R2+(chead(k,2)-ctail(k,1))**2 + END DO +!c! Pitagoras + R1 = dsqrt(R1) + R2 = dsqrt(R2) + +!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! Coulomb electrostatic interaction + Ecl = (332.0d0 * Qij) / Rhead +!c! derivative of Ecl is Gcl... + dGCLdR = (-332.0d0 * Qij ) / Rhead_sq + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + + ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq)) + Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0) + debkap=debaykapmart(itypi,itypj) + if (energy_dec) write(iout,*) "egb",Qij,debkap,Fgb,a12sq,ee0 + Egb = -(332.0d0 * Qij *& + (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb +! print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out +!c! Derivative of Egb is Ggb... + dGGBdFGB = -(-332.0d0 * Qij * & + (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)& + -(332.0d0 * Qij *& + (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb + dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb ) + dGGBdR = dGGBdFGB * dFGBdR +!c!------------------------------------------------------------------- +!c! Fisocav - isotropic cavity creation term +!c! or "how much energy it costs to put charged head in water" + pom = Rhead * csig + top = al1 * (dsqrt(pom) + al2 * pom - al3) + bot = (1.0d0 + al4 * pom**12.0d0) + botsq = bot * bot + FisoCav = top / bot +! write (*,*) "Rhead = ",Rhead +! write (*,*) "csig = ",csig +! write (*,*) "pom = ",pom +! write (*,*) "al1 = ",al1 +! write (*,*) "al2 = ",al2 +! write (*,*) "al3 = ",al3 +! write (*,*) "al4 = ",al4 +! write (*,*) "top = ",top +! write (*,*) "bot = ",bot +!c! Derivative of Fisocav is GCV... + dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2) + dbot = 12.0d0 * al4 * pom ** 11.0d0 + dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig +!c!------------------------------------------------------------------- +!c! Epol +!c! Polarization energy - charged heads polarize hydrophobic "neck" + MomoFac1 = (1.0d0 - chi1 * sqom2) + MomoFac2 = (1.0d0 - chi2 * sqom1) + RR1 = ( R1 * R1 ) / MomoFac1 + RR2 = ( R2 * R2 ) / MomoFac2 + ee1 = exp(-( RR1 / (4.0d0 * a12sq) )) + ee2 = exp(-( RR2 / (4.0d0 * a12sq) )) + fgb1 = sqrt( RR1 + a12sq * ee1 ) + fgb2 = sqrt( RR2 + a12sq * ee2 ) + epol = 332.0d0 * eps_inout_fac * ( & + (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 )) +!c! epol = 0.0d0 + dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)& + / (fgb1 ** 5.0d0) + dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)& + / (fgb2 ** 5.0d0) + dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )& + / ( 2.0d0 * fgb1 ) + dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )& + / ( 2.0d0 * fgb2 ) + dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))& + * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 ) + dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))& + * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 ) + dPOLdR1 = dPOLdFGB1 * dFGBdR1!*sss_ele_cut+epol*sss_ele_grad +!c! dPOLdR1 = 0.0d0 + dPOLdR2 = dPOLdFGB2 * dFGBdR2!*sss_ele_cut+epol*sss_ele_grad +!c! dPOLdR2 = 0.0d0 + dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 +!c! dPOLdOM1 = 0.0d0 + dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 +! epol=epol*sss_ele_cut +!c! dPOLdOM2 = 0.0d0 +!c!------------------------------------------------------------------- +!c! Elj +!c! Lennard-Jones 6-12 interaction between heads + pom = (pis / Rhead)**6.0d0 + Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) +!c! derivative of Elj is Glj + dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))& + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) +!c!------------------------------------------------------------------- +!c! Return the results +!c! These things do the dRdX derivatives, that is +!c! allow us to change what we see from function that changes with +!c! distance to function that changes with LOCATION (of the interaction +!c! site) + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1) + erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2) + 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) ) + federmaus = scalar(erhead_tail(1,1),dC_norm(1,j)) + eagle = scalar( erhead_tail(1,2), dC_norm(1,j) ) + adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) ) + facd1 = d1 * vbld_inv(i+nres) + facd2 = d2 * vbld_inv(j) + facd3 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres) + facd4 = dtailmart(2,itypi,itypj) * vbld_inv(j) + +!c! Now we add appropriate partial derivatives (one in each dimension) + DO k = 1, 3 + hawk = (erhead_tail(k,1) + & + facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) + condor = (erhead_tail(k,2) + & + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j))) + + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gradpepmartx(k,i) = gradpepmartx(k,i) & + +sss_ele_cut*(- dGCLdR * pom& + - dGGBdR * pom& + - dGCVdR * pom& + - dPOLdR1 * hawk& + - dPOLdR2 * (erhead_tail(k,2)& + -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))& + - dGLJdR * pom)-& + sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj) + + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j)) +! gradpepmartx(k,j) = gradpepmartx(k,j)+ dGCLdR * pom& +! + dGGBdR * pom+ dGCVdR * pom& +! + dPOLdR1 * (erhead_tail(k,1)& +! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j)))& +! + dPOLdR2 * condor + dGLJdR * pom + + gradpepmart(k,i) = gradpepmart(k,i) + & + sss_ele_cut*(- dGCLdR * erhead(k)& + - dGGBdR * erhead(k)& + - dGCVdR * erhead(k)& + - dPOLdR1 * erhead_tail(k,1)& + - dPOLdR2 * erhead_tail(k,2)& + - dGLJdR * erhead(k))& + - sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj) + + + gradpepmart(k,j) = gradpepmart(k,j) + & + sss_ele_cut*( dGCLdR * erhead(k) & + + dGGBdR * erhead(k) & + + dGCVdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1) & + + dPOLdR2 * erhead_tail(k,2)& + + dGLJdR * erhead(k))& + +sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj) + END DO + RETURN + END SUBROUTINE eqq_mart + + SUBROUTINE eqd_mart(Ecl,Elj,Epol) + use calc_data + use comm_momo + double precision facd4, federmaus,ecl,elj,epol + alphapol1 = alphapolmart(itypi,itypj) + w1 = wqdipmart(1,itypi,itypj) + w2 = wqdipmart(2,itypi,itypj) + pis = sig0headmart(itypi,itypj) + eps_head = epsheadmart(itypi,itypj) +! eps_head=0.0d0 +! w2=0.0d0 +! alphapol1=0.0d0 +!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 + R1=R1+(ctail(k,2)-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 * Qi * om1 + hawk = w2 * Qi * Qi * (1.0d0 - sqom2) + Ecl = sparrow / Rhead**2.0d0 & + - hawk / Rhead**4.0d0 + dGCLdR =sss_ele_cut*(-2.0d0 * sparrow / Rhead**3.0d0 & + + 4.0d0 * hawk / Rhead**5.0d0) +!c! dF/dom1 + dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = 0.0d0 ! + +!(2.0d0 * w2 * Qi * Qi * 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) + epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0) +!c! epol = 0.0d0 +!c!------------------------------------------------------------------ +!c! 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 = 0.0d0 ! as om2 is 0 +! (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) & +! * (2.0d0 - 0.5d0 * ee1) ) & +! / (2.0d0 * fgb1) + dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut +!c! dPOLdR1 = 0.0d0 + dPOLdOM1 = 0.0d0 +! dPOLdOM2 = dPOLdFGB1 * dFGBdOM2 + dPOLdOM2 = 0.0d0 +!c!------------------------------------------------------------------- +!c! Elj + pom = (pis / Rhead)**6.0d0 + Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) +!c! derivative of Elj is Glj + dGLJdR = 4.0d0 * eps_head*sss_ele_cut & + * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1) + END DO + + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) ) + facd1 = d1 * vbld_inv(i+nres) + + DO k = 1, 3 + hawk = (erhead_tail(k,1) + & + facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres))) + + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gradpepmartx(k,i) = gradpepmartx(k,i) & + - dGCLdR * pom& + - dPOLdR1 * hawk & + - dGLJdR * pom& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepmartx(k,j) = gradpepmartx(k,j) & +! + dGCLdR * pom & +! + dPOLdR1 * (erhead_tail(k,1) & +! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) & +! + dGLJdR * pom + + + gradpepmart(k,i) = gradpepmart(k,i) & + - dGCLdR * erhead(k) & + - dPOLdR1 * erhead_tail(k,1) & + - dGLJdR * erhead(k)& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + gradpepmart(k,j) = gradpepmart(k,j) & + + dGCLdR * erhead(k) & + + dPOLdR1 * erhead_tail(k,1) & + + dGLJdR * erhead(k)& + +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + END DO + RETURN + END SUBROUTINE eqd_mart + + SUBROUTINE edq_mart(Ecl,Elj,Epol) + use comm_momo + use calc_data + + double precision facd3, adler,ecl,elj,epol + alphapol2 = alphapolmart(itypi,itypj) + w1 = wqdipmart(1,itypi,itypj) + w2 = wqdipmart(2,itypi,itypj) + pis = sig0headmart(itypi,itypj) + eps_head = epsheadmart(itypi,itypj) +!c!------------------------------------------------------------------- +!c! R2 - distance between head of jth side chain and tail of ith sidechain + R2 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances + R2=R2+(chead(k,2)-ctail(k,1))**2 + END DO +!c! Pitagoras + R2 = dsqrt(R2) + +!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 +! write(iout,*) "KURWA2",Rhead + sparrow = w1 * Qj * om1 + hawk = w2 * Qj * Qj * (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)*sss_ele_cut +!c! dF/dom1 + dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0) +!c-------------------------------------------------------------------- +!c-------------------------------------------------------------------- +!c Polarization energy +!c Epol + MomoFac2 = (1.0d0 - chi2 * sqom1) + RR2 = R2 * R2 / MomoFac2 + ee2 = exp(-(RR2 / (4.0d0 * a12sq))) + fgb2 = sqrt(RR2 + a12sq * ee2) + epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 ) + dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) & + / (fgb2 ** 5.0d0) + dFGBdR2 = ( (R2 / MomoFac2) & + * ( 2.0d0 - (0.5d0 * ee2) ) ) & + / (2.0d0 * fgb2) + dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & + * (2.0d0 - 0.5d0 * ee2) ) & + / (2.0d0 * fgb2) + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut +!c! dPOLdR2 = 0.0d0 + dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 +!c! dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 +!c!------------------------------------------------------------------- +!c! Elj + pom = (pis / Rhead)**6.0d0 + Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) +!c! derivative of Elj is Glj + dGLJdR = 4.0d0 * eps_head & + * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut +!c!------------------------------------------------------------------- + +!c! Return the results +!c! (see comments in Eqq) + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2) + END DO + erdxi = scalar( erhead(1), dC_norm(1,i+nres) ) + erdxj = scalar( erhead(1), dC_norm(1,j) ) + eagle = scalar( erhead_tail(1,2), dC_norm(1,j) ) + adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) ) + facd1 = d1 * vbld_inv(i+nres) + facd2 = d2 * vbld_inv(j) + facd3 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres) + DO k = 1, 3 + condor = (erhead_tail(k,2) & + + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j))) + + pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres)) + gradpepmartx(k,i) = gradpepmartx(k,i) & + - dGCLdR * pom & + - dPOLdR2 * (erhead_tail(k,2) & + -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) & + - dGLJdR * pom& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j)) +! gradpepmartx(k,j) = gradpepmartx(k,j) & +! + dGCLdR * pom & +! + dPOLdR2 * condor & +! + dGLJdR * pom + + + gradpepmart(k,i) = gradpepmart(k,i) & + - dGCLdR * erhead(k) & + - dPOLdR2 * erhead_tail(k,2) & + - dGLJdR * erhead(k)& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + gradpepmart(k,j) = gradpepmart(k,j) & + + dGCLdR * erhead(k) & + + dPOLdR2 * erhead_tail(k,2) & + + dGLJdR * erhead(k)& + +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + END DO + RETURN + END SUBROUTINE edq_mart + + SUBROUTINE edq_mart_pep(Ecl,Elj,Epol) + use comm_momo + use calc_data + + double precision facd3, adler,ecl,elj,epol + alphapol2 = alphapolmart(itypi,itypj) + w1 = wqdipmart(1,itypi,itypj) + w2 = wqdipmart(2,itypi,itypj) + pis = sig0headmart(itypi,itypj) + eps_head = epsheadmart(itypi,itypj) +!c!------------------------------------------------------------------- +!c! R2 - distance between head of jth side chain and tail of ith sidechain + R2 = 0.0d0 + DO k = 1, 3 +!c! Calculate head-to-tail distances + R2=R2+(chead(k,2)-ctail(k,1))**2 + END DO +!c! Pitagoras + R2 = dsqrt(R2) + +!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 * Qj * om1 + hawk = w2 * Qj * Qj * (1.0d0 - sqom2) +! print *,"CO2", itypi,itypj +! print *,"CO?!.", w1,w2,Qj,om1 + 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)*sss_ele_cut +!c! dF/dom1 + dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0) +!c! dF/dom2 + dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0) +!c-------------------------------------------------------------------- +!c-------------------------------------------------------------------- +!c Polarization energy +!c Epol + MomoFac2 = (1.0d0 - chi2 * sqom1) + RR2 = R2 * R2 / MomoFac2 + ee2 = exp(-(RR2 / (4.0d0 * a12sq))) + fgb2 = sqrt(RR2 + a12sq * ee2) + epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 ) + dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) & + / (fgb2 ** 5.0d0) + dFGBdR2 = ( (R2 / MomoFac2) & + * ( 2.0d0 - (0.5d0 * ee2) ) ) & + / (2.0d0 * fgb2) + dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) & + * (2.0d0 - 0.5d0 * ee2) ) & + / (2.0d0 * fgb2) + dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut +!c! dPOLdR2 = 0.0d0 + dPOLdOM1 = dPOLdFGB2 * dFGBdOM1 +!c! dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 +!c!------------------------------------------------------------------- +!c! Elj + pom = (pis / Rhead)**6.0d0 + Elj = 4.0d0 * eps_head * pom * (pom-1.0d0) +!c! derivative of Elj is Glj + dGLJdR = 4.0d0 * eps_head*sss_ele_cut & + * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) & + + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0))) +!c!------------------------------------------------------------------- + +!c! Return the results +!c! (see comments in Eqq) + DO k = 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2) + END DO + erdxi = scalar( erhead(1), dC_norm(1,i) ) + facd1 = d1 * vbld_inv(i+1) + DO k = 1, 3 + pom = facd1*(erhead(k)-erdxi*dC_norm(k,i)) +! gradpepmartx(k,i) = gradpepmartx(k,i) & +! - dGCLdR * pom & +! - dPOLdR2 * (erhead_tail(k,2) & +! -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) & +! - dGLJdR * pom + +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j)) +! gradpepmartx(k,j) = gradpepmartx(k,j) & +! + dGCLdR * pom & +! + dPOLdR2 * condor & +! + dGLJdR * pom + + gradpepmart(k,i) = gradpepmart(k,i)+pom*(dGCLdR+dGLJdR) + gradpepmart(k,i+1) = gradpepmart(k,i+1)-pom*(dGCLdR+dGLJdR) + + gradpepmart(k,i) = gradpepmart(k,i) +0.5d0*( & + - dGCLdR * erhead(k) & + - dPOLdR2 * erhead_tail(k,2) & + - dGLJdR * erhead(k))& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + gradpepmart(k,i+1) = gradpepmart(k,i+1) +0.5d0*( & + - dGCLdR * erhead(k) & + - dPOLdR2 * erhead_tail(k,2) & + - dGLJdR * erhead(k))& + -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + + gradpepmart(k,j) = gradpepmart(k,j) & + + dGCLdR * erhead(k) & + + dPOLdR2 * erhead_tail(k,2) & + + dGLJdR * erhead(k)& + +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij + + + END DO + RETURN + END SUBROUTINE edq_mart_pep +!-------------------------------------------------------------------------- + + SUBROUTINE edd_mart(ECL) +! IMPLICIT NONE + use comm_momo + use calc_data + + double precision ecl +!c! csig = sigiso(itypi,itypj) + w1 = wqdipmart(1,itypi,itypj) + w2 = wqdipmart(2,itypi,itypj) +! w2=0.0d0 +!c!------------------------------------------------------------------- +!c! ECL +! print *,"om1",om1,om2,om12 + fac = - 3.0d0 * om1 !after integer and simplify + c1 = (w1 / (Rhead**3.0d0)) * fac + c2 = (w2 / Rhead ** 6.0d0) & + * (4.0d0 + 6.0d0*sqom1 ) !after integration and simplifimartion + ECL = c1 - c2 +!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 + 6.0d0*sqom1) + dGCLdR = (c1 - c2)*sss_ele_cut +!c! dECL/dom1 + c1 = (-3.0d0 * w1) / (Rhead**3.0d0) + c2 = (12.0d0 * w2*om1) / (Rhead**6.0d0) + dGCLdOM1 = c1 - c2 +!c! dECL/dom2 +! c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0) + c1=0.0 ! this is because om2 is 0 +! c2 = (-6.0d0 * w2) / (Rhead**6.0d0) & +! * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 ) + c2=0.0 !om is 0 + dGCLdOM2 = c1 - c2 +!c! dECL/dom12 +! c1 = w1 / (Rhead ** 3.0d0) + c1=0.0d0 ! this is because om12 is 0 +! c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + c2=0.0d0 !om12 is 0 + dGCLdOM12 = c1 - c2 +!c!------------------------------------------------------------------- +!c! Return the results +!c! (see comments in Eqq) + 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)) + gradpepmartx(k,i) = gradpepmartx(k,i) - dGCLdR * pom& + -ecl*sss_ele_grad*rij*rreal(k) +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepmartx(k,j) = gradpepmartx(k,j) + dGCLdR * pom + + gradpepmart(k,i) = gradpepmart(k,i) - dGCLdR * erhead(k)& + -ecl*sss_ele_grad*rij*rreal(k) + + gradpepmart(k,j) = gradpepmart(k,j) + dGCLdR * erhead(k)& + +ecl*sss_ele_grad*rij*rreal(k) + + END DO + RETURN + END SUBROUTINE edd_mart + SUBROUTINE edd_mart_pep(ECL) +! IMPLICIT NONE + use comm_momo + use calc_data + + double precision ecl +!c! csig = sigiso(itypi,itypj) + w1 = wqdipmart(1,itypi,itypj) + w2 = wqdipmart(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)) + ECL = c1 - c2 +!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)) + dGCLdR = (c1 - c2)*sss_ele_cut +!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 ) + dGCLdOM1 = c1 - c2 +!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 ) + dGCLdOM2 = c1 - c2 + dGCLdOM2=0.0d0 ! this is because om2=0 +!c! dECL/dom12 + c1 = w1 / (Rhead ** 3.0d0) + c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0 + dGCLdOM12 = c1 - c2 + dGCLdOM12=0.0d0 !this is because om12=0.0 +!c!------------------------------------------------------------------- +!c! Return the results +!c! (see comments in Eqq) + DO k= 1, 3 + erhead(k) = Rhead_distance(k)/Rhead + END DO + erdxi = scalar( erhead(1), dC_norm(1,i) ) + erdxj = scalar( erhead(1), dC_norm(1,j+nres) ) + facd1 = d1 * vbld_inv(i) + facd2 = d2 * vbld_inv(j+nres) + DO k = 1, 3 + + pom = facd1*(erhead(k)-erdxi*dC_norm(k,i)) + gradpepmart(k,i) = gradpepmart(k,i) + dGCLdR * pom + gradpepmart(k,i+1) = gradpepmart(k,i+1) - dGCLdR * pom +! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres)) +! gradpepmartx(k,j) = gradpepmartx(k,j) + dGCLdR * pom + + gradpepmart(k,i) = gradpepmart(k,i) - dGCLdR * erhead(k)*0.5d0& + -ECL*sss_ele_grad*rreal(k)*rij + gradpepmart(k,i+1) = gradpepmart(k,i+1)- dGCLdR * erhead(k)*0.5d0& + -ECL*sss_ele_grad*rreal(k)*rij + + gradpepmart(k,j) = gradpepmart(k,j) + dGCLdR * erhead(k)& + +ECL*sss_ele_grad*rreal(k)*rij + + END DO + RETURN + END SUBROUTINE edd_mart_pep + + SUBROUTINE elgrad_init_mart(eheadtail,Egb,Ecl,Elj,Equad,Epol) + use comm_momo + use calc_data + real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb + eps_out=80.0d0 + itypi = itype(i,1) + itypj = itype(j,4) +! print *,"in elegrad",i,j,itypi,itypj +!c! 1/(Gas Constant * Thermostate temperature) = BetaT +!c! ENABLE THIS LINE WHEN USING CHECKGRAD!!! +!c! t_bath = 300 +!c! BetaT = 1.0d0 / (t_bath * Rb)i + Rb=0.001986d0 + BetaT = 1.0d0 / (298.0d0 * Rb) +!c! Gay-berne var's + sig0ij = sigmamart( itypi,itypj ) + chi1 = chi1mart( itypi, itypj ) + chi2 = 0.0d0 + chi12 = 0.0d0 + chip1 = chipp1mart( itypi, itypj ) + chip2 = 0.0d0 + chip12 = 0.0d0 +!c! not used by momo potential, but needed by sc_angular which is shared +!c! by all energy_potential subroutines + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + dxj = 0.0d0 !dc_norm( 1, nres+j ) + dyj = 0.0d0 !dc_norm( 2, nres+j ) + dzj = 0.0d0 !dc_norm( 3, nres+j ) +! print *,"before dheadmart" +!c! distance from center of chain(?) to polar/charged head + d1 = dheadmart(1, 1, itypi, itypj) + d2 = dheadmart(2, 1, itypi, itypj) +!c! ai*aj from Fgb + a12sq = rborn1mart(itypi,itypj) * rborn2mart(itypi,itypj) +!c! a12sq = a12sq * a12sq +!c! charge of amino acid itypi is... +! print *,"after dheadmart" + Qi = icharge(itypi) + Qj = ichargelipid(itypj) + Qij = Qi * Qj +! print *,"after icharge" + +!c! chis1,2,12 + chis1 = chis1mart(itypi,itypj) + chis2 = 0.0d0 + chis12 = 0.0d0 + sig1 = sigmap1mart(itypi,itypj) + sig2 = sigmap2mart(itypi,itypj) +! print *,"before alphasurmart" +!c! alpha factors from Fcav/Gcav + b1cav = alphasurmart(1,itypi,itypj) + b2cav = alphasurmart(2,itypi,itypj) + b3cav = alphasurmart(3,itypi,itypj) + b4cav = alphasurmart(4,itypi,itypj) + wqd = wquadmart(itypi, itypj) +! print *,"after alphasurmar n wquad" +!c! used by Fgb + eps_in = epsintabmart(itypi,itypj) + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +!c!------------------------------------------------------------------- +!c! tail lomartion and distance calculations + Rtail = 0.0d0 + DO k = 1, 3 + ctail(k,1)=c(k,i+nres)-dtailmart(1,itypi,itypj)*dc_norm(k,nres+i) + ctail(k,2)=c(k,j)!-dtailmart(2,itypi,itypj)*dc_norm(k,nres+j) + END DO +!c! tail distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 ) + Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 ) + Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 ) + Rtail = dsqrt( & + (Rtail_distance(1)*Rtail_distance(1)) & + + (Rtail_distance(2)*Rtail_distance(2)) & + + (Rtail_distance(3)*Rtail_distance(3))) +!c!------------------------------------------------------------------- +!c! Calculate lomartion and distance between polar heads +!c! distance between heads +!c! for each one of our three dimensional space... + d1 = dheadmart(1, 1, itypi, itypj) + d2 = dheadmart(2, 1, itypi, itypj) + + DO k = 1,3 +!c! lomartion of polar head is computed by taking hydrophobic centre +!c! and moving by a d1 * dc_norm vector +!c! see unres publimartions for very informative images + chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres) + chead(k,2) = c(k, j) +!c! distance +!c! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +!c! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + Rhead_distance(k) = chead(k,2) - chead(k,1) + END DO +!c! 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))) +!c!------------------------------------------------------------------- +!c! zero everything that should be zero'ed + Egb = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + eheadtail = 0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + RETURN + END SUBROUTINE elgrad_init_mart + + SUBROUTINE elgrad_init_mart_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol) + use comm_momo + use calc_data + real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb + eps_out=80.0d0 + itypi = 10 + itypj = itype(j,4) +!c! 1/(Gas Constant * Thermostate temperature) = BetaT +!c! ENABLE THIS LINE WHEN USING CHECKGRAD!!! +!c! t_bath = 300 +!c! BetaT = 1.0d0 / (t_bath * Rb)i + Rb=0.001986d0 + BetaT = 1.0d0 / (298.0d0 * Rb) +!c! Gay-berne var's + sig0ij = sigmamart( itypi,itypj ) + chi1 = chi1mart( itypi, itypj ) + chi2 = 0.0d0 + chi12 = 0.0d0 + chip1 = chipp1mart( itypi, itypj ) + chip2 = 0.0d0 + chip12 = 0.0d0 +!c! not used by momo potential, but needed by sc_angular which is shared +!c! by all energy_potential subroutines + alf1 = 0.0d0 + alf2 = 0.0d0 + alf12 = 0.0d0 + dxj = 0.0d0 !dc_norm( 1, nres+j ) + dyj = 0.0d0 !dc_norm( 2, nres+j ) + dzj = 0.0d0 !dc_norm( 3, nres+j ) +!c! distance from center of chain(?) to polar/charged head + d1 = dheadmart(1, 1, itypi, itypj) + d2 = dheadmart(2, 1, itypi, itypj) +!c! ai*aj from Fgb + a12sq = rborn1mart(itypi,itypj) * rborn2mart(itypi,itypj) +!c! a12sq = a12sq * a12sq +!c! charge of amino acid itypi is... + Qi = 0 + Qj = ichargelipid(itypj) +! Qij = Qi * Qj +!c! chis1,2,12 + chis1 = chis1mart(itypi,itypj) + chis2 = 0.0d0 + chis12 = 0.0d0 + sig1 = sigmap1mart(itypi,itypj) + sig2 = sigmap2mart(itypi,itypj) +!c! alpha factors from Fcav/Gcav + b1cav = alphasurmart(1,itypi,itypj) + b2cav = alphasurmart(2,itypi,itypj) + b3cav = alphasurmart(3,itypi,itypj) + b4cav = alphasurmart(4,itypi,itypj) + wqd = wquadmart(itypi, itypj) +!c! used by Fgb + eps_in = epsintabmart(itypi,itypj) + eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out)) +!c!------------------------------------------------------------------- +!c! tail lomartion and distance calculations + Rtail = 0.0d0 + DO k = 1, 3 + ctail(k,1)=(c(k,i)+c(k,i+1))/2.0-dtailmart(1,itypi,itypj)*dc_norm(k,i) + ctail(k,2)=c(k,j)!-dtailmart(2,itypi,itypj)*dc_norm(k,nres+j) + END DO +!c! tail distances will be themselves usefull elswhere +!c1 (in Gcav, for example) + Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 ) + Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 ) + Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 ) + Rtail = dsqrt( & + (Rtail_distance(1)*Rtail_distance(1)) & + + (Rtail_distance(2)*Rtail_distance(2)) & + + (Rtail_distance(3)*Rtail_distance(3))) +!c!------------------------------------------------------------------- +!c! Calculate lomartion and distance between polar heads +!c! distance between heads +!c! for each one of our three dimensional space... + d1 = dheadmart(1, 1, itypi, itypj) + d2 = dheadmart(2, 1, itypi, itypj) + + DO k = 1,3 +!c! lomartion of polar head is computed by taking hydrophobic centre +!c! and moving by a d1 * dc_norm vector +!c! see unres publimartions for very informative images + chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i) + chead(k,2) = c(k, j) +!c! distance +!c! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres)) +!c! Rsc(k) = Rsc_distance(k) * Rsc_distance(k) + Rhead_distance(k) = chead(k,2) - chead(k,1) + END DO +!c! 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))) +!c!------------------------------------------------------------------- +!c! zero everything that should be zero'ed + Egb = 0.0d0 + ECL = 0.0d0 + Elj = 0.0d0 + Equad = 0.0d0 + Epol = 0.0d0 + eheadtail = 0.0d0 + dGCLdOM1 = 0.0d0 + dGCLdOM2 = 0.0d0 + dGCLdOM12 = 0.0d0 + dPOLdOM1 = 0.0d0 + dPOLdOM2 = 0.0d0 + RETURN + END SUBROUTINE elgrad_init_mart_pep + + subroutine sc_grad_mart + use calc_data + real(kind=8), dimension(3) :: dcosom1,dcosom2 + 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 +! diagnostics only +! eom1=0.0d0 +! eom2=0.0d0 +! eom12=evdwij*eps1_om12 +! end diagnostics + + 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)) + enddo + do k=1,3 + gg(k)=(gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)) +! print *,'gg',k,gg(k) + enddo +! print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut +! write (iout,*) "gg",(gg(k),k=1,3) + do k=1,3 + gradpepmartx(k,i)=gradpepmartx(k,i)-gg(k)*sss_ele_cut & + +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) & + +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut + +! gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) & +! +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) & +! +eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv + +! write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) & +! +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv +! write (iout,*)(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) & +! +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv + enddo +! +! Calculate the components of the gradient in DC and X +! + do l=1,3 + gradpepmart(l,i)=gradpepmart(l,i)-gg(l)*sss_ele_cut + gradpepmart(l,j)=gradpepmart(l,j)+gg(l)*sss_ele_cut + enddo + end subroutine sc_grad_mart + + subroutine sc_grad_mart_pep + use calc_data + real(kind=8), dimension(3) :: dcosom1,dcosom2 + 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 +! diagnostics only +! eom1=0.0d0 +! eom2=0.0d0 +! eom12=evdwij*eps1_om12 +! end diagnostics +! write (iout,*) "gg",(gg(k),k=1,3) + + 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) + gradpepmart(k,i)= gradpepmart(k,i) +sss_ele_cut*(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) + gradpepmart(k,i+1)= gradpepmart(k,i+1) +sss_ele_cut*(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) + gradpepmart(k,j)=gradpepmart(k,j)+gg(k)*sss_ele_cut + enddo + end subroutine sc_grad_mart_pep end module energy