gshieldc_ec,gshieldc_loc_ec,gshieldx_t3, &
gshieldc_t3,gshieldc_loc_t3,gshieldx_t4,gshieldc_t4, &
gshieldc_loc_t4,gshieldx_ll,gshieldc_ll,gshieldc_loc_ll,&
- grad_shield !(3,maxres)
+ grad_shield,gg_tube,gg_tube_sc !(3,maxres)
! real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2)
real(kind=8),dimension(:,:),allocatable :: gel_loc,gel_loc_long,&
gcorr3_turn,gcorr4_turn,gcorr6_turn,gradb,gradbx !(3,maxres)
integer :: n_corr,n_corr1,ierror
real(kind=8) :: etors,edihcnstr,etors_d,esccor,ehpb
real(kind=8) :: evdw,evdw1,evdw2,evdw2_14,escloc,ees,eel_loc
- real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran
+ real(kind=8) :: eello_turn3,eello_turn4,estr,ebe,eliptran,etube
real(kind=8) :: ecorr,ecorr5,ecorr6,eturn6
#ifdef MPI
else
eliptran=0.0d0
endif
+ if (tubemode.eq.1) then
+ call calctube(etube)
+ else if (tubemode.eq.2) then
+ call calctube2(etube)
+ elseif (tubemode.eq.3) then
+ call calcnano(etube)
+ else
+ etube=0.0d0
+ endif
#ifdef TIMING
time_enecalc=time_enecalc+MPI_Wtime()-time00
energia(20)=Uconst+Uconst_back
energia(21)=esccor
energia(22)=eliptran
+ energia(25)=etube
! Here are the energies showed per procesor if the are more processors
! per molecule then we sum it up in sum_energy subroutine
! print *," Processor",myrank," calls SUM_ENERGY"
real(kind=8) :: evdw,evdw2,evdw2_14,ees,evdw1,ecorr,ecorr5,ecorr6
real(kind=8) :: eel_loc,eello_turn3,eello_turn4,eturn6,ebe,escloc
real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,esccor,etot, &
- eliptran
+ eliptran,etube
integer :: i
#ifdef MPI
integer :: ierr
Uconst=energia(20)
esccor=energia(21)
eliptran=energia(22)
+ etube=energia(25)
#ifdef SPLITELE
etot=wsc*evdw+wscp*evdw2+welec*ees+wvdwpp*evdw1 &
+wang*ebe+wtor*etors+wscloc*escloc &
+wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
- +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
+ +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube
#else
etot=wsc*evdw+wscp*evdw2+welec*(ees+evdw1) &
+wang*ebe+wtor*etors+wscloc*escloc &
+wstrain*ehpb+wcorr*ecorr+wcorr5*ecorr5 &
+wcorr6*ecorr6+wturn4*eello_turn4+wturn3*eello_turn3 &
+wturn6*eturn6+wel_loc*eel_loc+edihcnstr+wtor_d*etors_d &
- +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran
+ +wbond*estr+Uconst+wsccor*esccor+wliptran*eliptran+wtube*etube
#endif
energia(0)=etot
! detecting NaNQ
!el local variables
real(kind=8) :: etot,evdw,evdw2,ees,evdw1,ecorr,ecorr5,ecorr6,eel_loc
real(kind=8) :: eello_turn6,eello_turn3,eello_turn4,ebe,escloc
- real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran
+ real(kind=8) :: etors,etors_d,ehpb,edihcnstr,estr,Uconst,esccor,eliptran,&
+ etube
etot=energia(0)
evdw=energia(1)
Uconst=energia(20)
esccor=energia(21)
eliptran=energia(22)
-
+ etube=energia(25)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
estr,wbond,ebe,wang,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,&
edihcnstr,ebr*nss,&
- Uconst,eliptran,wliptran,etot
+ Uconst,eliptran,wliptran,etube,wtube,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ &
'UCONST= ',1pE16.6,' (Constraint energy)'/ &
'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/&
+ 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ &
'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
ecorr,wcorr,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,&
- ebr*nss,Uconst,eliptran,wliptran,etot
+ ebr*nss,Uconst,eliptran,wliptran,etube,wtube,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/ &
'UCONST=',1pE16.6,' (Constraint energy)'/ &
'ELT=',1pE16.6, ' WEIGHT=',1pD16.6,' (Lipid transfer energy)'/ &
+ 'ETUBE=',1pE16.6, ' WEIGHT=',1pD16.6,' (cylindrical energy)'/ &
'ETOT= ',1pE16.6,' (total)')
#endif
return
+wcorr*gshieldc_ec(j,i) &
+wturn3*gshieldc_t3(j,i)&
+wturn4*gshieldc_t4(j,i)&
- +wel_loc*gshieldc_ll(j,i)
+ +wel_loc*gshieldc_ll(j,i)&
+ +wtube*gg_tube(j,i)
+
enddo
+welec*gshieldc(j,i)&
+wcorr*gshieldc_ec(j,i) &
+wturn4*gshieldc_t4(j,i) &
- +wel_loc*gshieldc_ll(j,i)
+ +wel_loc*gshieldc_ll(j,i)&
+ +wtube*gg_tube(j,i)
+
enddo
+wturn4*gshieldc_t4(j,i) &
+wturn4*gshieldc_loc_t4(j,i) &
+wel_loc*gshieldc_ll(j,i) &
- +wel_loc*gshieldc_loc_ll(j,i)
+ +wel_loc*gshieldc_loc_ll(j,i) &
+ +wtube*gg_tube(j,i)
+
#else
gradc(j,i,icg)=gradbufc(j,i)+welec*gelc(j,i)+ &
+wturn4*gshieldc_t4(j,i) &
+wturn4*gshieldc_loc_t4(j,i) &
+wel_loc*gshieldc_ll(j,i) &
- +wel_loc*gshieldc_loc_ll(j,i)
+ +wel_loc*gshieldc_loc_ll(j,i) &
+ +wtube*gg_tube(j,i)
+
#endif
+wcorr*gshieldx_ec(j,i) &
+wturn3*gshieldx_t3(j,i) &
+wturn4*gshieldx_t4(j,i) &
- +wel_loc*gshieldx_ll(j,i)
+ +wel_loc*gshieldx_ll(j,i)&
+ +wtube*gg_tube_sc(j,i)
+
enddo
enddo
gshieldx_ll(j,i)=0.0d0
gshieldc_ll(j,i)=0.0d0
gshieldc_loc_ll(j,i)=0.0d0
-
+ gg_tube(j,i)=0.0d0
+ gg_tube_sc(j,i)=0.0d0
do intertyp=1,3
gloc_sc(intertyp,i,icg)=0.0d0
enddo
enddo
return
end subroutine Eliptransfer
+!----------------------------------NANO FUNCTIONS
+!C-----------------------------------------------------------------------
+!C-----------------------------------------------------------
+!C This subroutine is to mimic the histone like structure but as well can be
+!C utilizet to nanostructures (infinit) small modification has to be used to
+!C make it finite (z gradient at the ends has to be changes as well as the x,y
+!C gradient has to be modified at the ends
+!C The energy function is Kihara potential
+!C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6)
+!C 4eps is depth of well sigma is r_minimum r is distance from center of tube
+!C and r0 is the excluded size of nanotube (can be set to 0 if we want just a
+!C simple Kihara potential
+ subroutine calctube(Etube)
+ real(kind=8) :: vectube(3),enetube(nres*2)
+ real(kind=8) :: Etube,xtemp,xminact,yminact,&
+ ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi, &
+ sc_aa_tube,sc_bb_tube
+ integer :: i,j,iti
+ Etube=0.0d0
+ do i=itube_start,itube_end
+ enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
+ enddo
+!C first we calculate the distance from tube center
+!C for UNRES
+ do i=itube_start,itube_end
+!C lets ommit dummy atoms for now
+ if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+!C now calculate distance from center of tube and direction vectors
+ xmin=boxxsize
+ ymin=boxysize
+! Find minimum distance in periodic box
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+
+!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
+!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
+
+!C as the tube is infinity we do not calculate the Z-vector use of Z
+!C as chosen axis
+ vectube(3)=0.0d0
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+!C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
+!C write(iout,*) "TU13",i,rdiff6,enetube(i)
+!C print *,rdiff,rdiff6,pep_aa_tube
+!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+!C now we calculate gradient
+ fac=(-12.0d0*pep_aa_tube/rdiff6- &
+ 6.0d0*pep_bb_tube)/rdiff6/rdiff
+!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
+!C &rdiff,fac
+!C now direction of gg_tube vector
+ do j=1,3
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+ gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+ enddo
+ enddo
+!C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
+!C print *,gg_tube(1,0),"TU"
+
+
+ do i=itube_start,itube_end
+!C Lets not jump over memory as we use many times iti
+ iti=itype(i)
+!C lets ommit dummy atoms for now
+ if ((iti.eq.ntyp1) &
+!C in UNRES uncomment the line below as GLY has no side-chain...
+!C .or.(iti.eq.10)
+ ) cycle
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i+nres)),boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i+nres)),boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+!C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
+!C & tubecenter(2)
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+
+!C as the tube is infinity we do not calculate the Z-vector use of Z
+!C as chosen axis
+ vectube(3)=0.0d0
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+!C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ sc_aa_tube=sc_aa_tube_par(iti)
+ sc_bb_tube=sc_bb_tube_par(iti)
+ enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
+ fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- &
+ 6.0d0*sc_bb_tube/rdiff6/rdiff
+!C now direction of gg_tube vector
+ do j=1,3
+ gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+ enddo
+ enddo
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
+ enddo
+!C print *,"ETUBE", etube
+ return
+ end subroutine calctube
+!C TO DO 1) add to total energy
+!C 2) add to gradient summation
+!C 3) add reading parameters (AND of course oppening of PARAM file)
+!C 4) add reading the center of tube
+!C 5) add COMMONs
+!C 6) add to zerograd
+!C 7) allocate matrices
+
+
+!C-----------------------------------------------------------------------
+!C-----------------------------------------------------------
+!C This subroutine is to mimic the histone like structure but as well can be
+!C utilizet to nanostructures (infinit) small modification has to be used to
+!C make it finite (z gradient at the ends has to be changes as well as the x,y
+!C gradient has to be modified at the ends
+!C The energy function is Kihara potential
+!C E=4esp*((sigma/(r-r0))^12 - (sigma/(r-r0))^6)
+!C 4eps is depth of well sigma is r_minimum r is distance from center of tube
+!C and r0 is the excluded size of nanotube (can be set to 0 if we want just a
+!C simple Kihara potential
+ subroutine calctube2(Etube)
+ real(kind=8) :: vectube(3),enetube(nres*2)
+ real(kind=8) :: Etube,xtemp,xminact,yminact,&
+ ytemp,xmin,ymin,tub_r,rdiff,rdiff6,fac,positi,fracinbuf,&
+ sstube,ssgradtube,sc_aa_tube,sc_bb_tube
+ integer:: i,j,iti
+ Etube=0.0d0
+ do i=itube_start,itube_end
+ enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
+ enddo
+!C first we calculate the distance from tube center
+!C first sugare-phosphate group for NARES this would be peptide group
+!C for UNRES
+ do i=itube_start,itube_end
+!C lets ommit dummy atoms for now
+
+ if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+!C now calculate distance from center of tube and direction vectors
+!C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+!C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+!C vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+!C if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+
+!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
+!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
+
+!C as the tube is infinity we do not calculate the Z-vector use of Z
+!C as chosen axis
+ vectube(3)=0.0d0
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+!C THIS FRAGMENT MAKES TUBE FINITE
+ positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ if (positi.le.0) positi=positi+boxzsize
+!C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+!c for each residue check if it is in lipid or lipid water border area
+!C respos=mod(c(3,i+nres),boxzsize)
+!C print *,positi,bordtubebot,buftubebot,bordtubetop
+ if ((positi.gt.bordtubebot) &
+ .and.(positi.lt.bordtubetop)) then
+!C the energy transfer exist
+ if (positi.lt.buftubebot) then
+ fracinbuf=1.0d0- &
+ ((positi-bordtubebot)/tubebufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+!C print *,ssgradtube, sstube,tubetranene(itype(i))
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+!C &+ssgradtube*tubetranene(itype(i))
+!C gg_tube(3,i-1)= gg_tube(3,i-1)
+!C &+ssgradtube*tubetranene(itype(i))
+!C print *,"doing sccale for lower part"
+ elseif (positi.gt.buftubetop) then
+ fracinbuf=1.0d0- &
+ ((bordtubetop-positi)/tubebufthick)
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+!C &+ssgradtube*tubetranene(itype(i))
+!C gg_tube(3,i-1)= gg_tube(3,i-1)
+!C &+ssgradtube*tubetranene(itype(i))
+!C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ sstube=1.0d0
+ ssgradtube=0.0d0
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+!C print *,"I am in true lipid"
+ endif
+ else
+!C sstube=0.0d0
+!C ssgradtube=0.0d0
+ cycle
+ endif ! if in lipid or buffor
+
+!C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ enetube(i)=enetube(i)+sstube* &
+ (pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6)
+!C write(iout,*) "TU13",i,rdiff6,enetube(i)
+!C print *,rdiff,rdiff6,pep_aa_tube
+!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+!C now we calculate gradient
+ fac=(-12.0d0*pep_aa_tube/rdiff6- &
+ 6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube
+!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
+!C &rdiff,fac
+
+!C now direction of gg_tube vector
+ do j=1,3
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+ gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+ enddo
+ gg_tube(3,i)=gg_tube(3,i) &
+ +ssgradtube*enetube(i)/sstube/2.0d0
+ gg_tube(3,i-1)= gg_tube(3,i-1) &
+ +ssgradtube*enetube(i)/sstube/2.0d0
+
+ enddo
+!C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
+!C print *,gg_tube(1,0),"TU"
+ do i=itube_start,itube_end
+!C Lets not jump over memory as we use many times iti
+ iti=itype(i)
+!C lets ommit dummy atoms for now
+ if ((iti.eq.ntyp1) &
+!!C in UNRES uncomment the line below as GLY has no side-chain...
+ .or.(iti.eq.10) &
+ ) cycle
+ vectube(1)=c(1,i+nres)
+ vectube(1)=mod(vectube(1),boxxsize)
+ if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+ vectube(2)=c(2,i+nres)
+ vectube(2)=mod(vectube(2),boxysize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+!C THIS FRAGMENT MAKES TUBE FINITE
+ positi=(mod(c(3,i+nres),boxzsize))
+ if (positi.le.0) positi=positi+boxzsize
+!C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+!c for each residue check if it is in lipid or lipid water border area
+!C respos=mod(c(3,i+nres),boxzsize)
+!C print *,positi,bordtubebot,buftubebot,bordtubetop
+
+ if ((positi.gt.bordtubebot) &
+ .and.(positi.lt.bordtubetop)) then
+!C the energy transfer exist
+ if (positi.lt.buftubebot) then
+ fracinbuf=1.0d0- &
+ ((positi-bordtubebot)/tubebufthick)
+!C lipbufthick is thickenes of lipid buffore
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+!C print *,ssgradtube, sstube,tubetranene(itype(i))
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+!C &+ssgradtube*tubetranene(itype(i))
+!C gg_tube(3,i-1)= gg_tube(3,i-1)
+!C &+ssgradtube*tubetranene(itype(i))
+!C print *,"doing sccale for lower part"
+ elseif (positi.gt.buftubetop) then
+ fracinbuf=1.0d0- &
+ ((bordtubetop-positi)/tubebufthick)
+
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+!C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+!C &+ssgradtube*tubetranene(itype(i))
+!C gg_tube(3,i-1)= gg_tube(3,i-1)
+!C &+ssgradtube*tubetranene(itype(i))
+!C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ sstube=1.0d0
+ ssgradtube=0.0d0
+ enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
+!C print *,"I am in true lipid"
+ endif
+ else
+!C sstube=0.0d0
+!C ssgradtube=0.0d0
+ cycle
+ endif ! if in lipid or buffor
+!CEND OF FINITE FRAGMENT
+!C as the tube is infinity we do not calculate the Z-vector use of Z
+!C as chosen axis
+ vectube(3)=0.0d0
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+!C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ sc_aa_tube=sc_aa_tube_par(iti)
+ sc_bb_tube=sc_bb_tube_par(iti)
+ enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)&
+ *sstube+enetube(i+nres)
+!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+!C now we calculate gradient
+ fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-&
+ 6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube
+!C now direction of gg_tube vector
+ do j=1,3
+ gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+ enddo
+ gg_tube_SC(3,i)=gg_tube_SC(3,i) &
+ +ssgradtube*enetube(i+nres)/sstube
+ gg_tube(3,i-1)= gg_tube(3,i-1) &
+ +ssgradtube*enetube(i+nres)/sstube
+
+ enddo
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
+ enddo
+!C print *,"ETUBE", etube
+ return
+ end subroutine calctube2
+!=====================================================================================================================================
+ subroutine calcnano(Etube)
+ real(kind=8) :: vectube(3),enetube(nres*2), &
+ enecavtube(nres*2)
+ 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
+
+ Etube=0.0d0
+ print *,itube_start,itube_end,"poczatek"
+ do i=itube_start,itube_end
+ enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
+ enddo
+!C first we calculate the distance from tube center
+!C first sugare-phosphate group for NARES this would be peptide group
+!C for UNRES
+ do i=itube_start,itube_end
+!C lets ommit dummy atoms for now
+ if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
+!C now calculate distance from center of tube and direction vectors
+ xmin=boxxsize
+ ymin=boxysize
+ zmin=boxzsize
+
+ do j=-1,1
+ vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+ vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ vectube(3)=vectube(3)+boxzsize*j
+
+
+ xminact=dabs(vectube(1)-tubecenter(1))
+ yminact=dabs(vectube(2)-tubecenter(2))
+ zminact=dabs(vectube(3)-tubecenter(3))
+
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ if (zmin.gt.zminact) then
+ zmin=zminact
+ ztemp=vectube(3)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(3)=ztemp
+
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+ vectube(3)=vectube(3)-tubecenter(3)
+
+!C print *,"x",(c(1,i)+c(1,i+1))/2.0d0,tubecenter(1)
+!C print *,"y",(c(2,i)+c(2,i+1))/2.0d0,tubecenter(2)
+!C as the tube is infinity we do not calculate the Z-vector use of Z
+!C as chosen axis
+!C vectube(3)=0.0d0
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+ vectube(3)=vectube(3)/tub_r
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+!C for vectorization reasons we will sumup at the end to avoid depenence of previous
+ enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
+!C write(iout,*) "TU13",i,rdiff6,enetube(i)
+!C print *,rdiff,rdiff6,pep_aa_tube
+!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+!C now we calculate gradient
+ fac=(-12.0d0*pep_aa_tube/rdiff6- &
+ 6.0d0*pep_bb_tube)/rdiff6/rdiff
+!C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
+!C &rdiff,fac
+ if (acavtubpep.eq.0.0d0) then
+!C go to 667
+ enecavtube(i)=0.0
+ faccav=0.0
+ else
+ denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6)
+ enecavtube(i)= &
+ (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep) &
+ /denominator
+ enecavtube(i)=0.0
+ faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff)) &
+ *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff) &
+ +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0) &
+ /denominator**2.0d0
+!C faccav=0.0
+!C fac=fac+faccav
+!C 667 continue
+ endif
+
+ do j=1,3
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
+ gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
+ enddo
+ enddo
+
+ do i=itube_start,itube_end
+ enecavtube(i)=0.0d0
+!C Lets not jump over memory as we use many times iti
+ iti=itype(i)
+!C lets ommit dummy atoms for now
+ if ((iti.eq.ntyp1) &
+!C in UNRES uncomment the line below as GLY has no side-chain...
+!C .or.(iti.eq.10)
+ ) cycle
+ xmin=boxxsize
+ ymin=boxysize
+ zmin=boxzsize
+ do j=-1,1
+ vectube(1)=dmod((c(1,i+nres)),boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=dmod((c(2,i+nres)),boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+ vectube(3)=dmod((c(3,i+nres)),boxzsize)
+ vectube(3)=vectube(3)+boxzsize*j
+
+
+ xminact=dabs(vectube(1)-tubecenter(1))
+ yminact=dabs(vectube(2)-tubecenter(2))
+ zminact=dabs(vectube(3)-tubecenter(3))
+
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ if (zmin.gt.zminact) then
+ zmin=zminact
+ ztemp=vectube(3)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+ vectube(3)=ztemp
+
+!C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
+!C & tubecenter(2)
+ vectube(1)=vectube(1)-tubecenter(1)
+ vectube(2)=vectube(2)-tubecenter(2)
+ vectube(3)=vectube(3)-tubecenter(3)
+!C now calculte the distance
+ tub_r=dsqrt(vectube(1)**2+vectube(2)**2+vectube(3)**2)
+!C now normalize vector
+ vectube(1)=vectube(1)/tub_r
+ vectube(2)=vectube(2)/tub_r
+ vectube(3)=vectube(3)/tub_r
+
+!C calculte rdiffrence between r and r0
+ rdiff=tub_r-tubeR0
+!C and its 6 power
+ rdiff6=rdiff**6.0d0
+ sc_aa_tube=sc_aa_tube_par(iti)
+ sc_bb_tube=sc_bb_tube_par(iti)
+ enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
+!C enetube(i+nres)=0.0d0
+!C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
+!C now we calculate gradient
+ fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff- &
+ 6.0d0*sc_bb_tube/rdiff6/rdiff
+!C fac=0.0
+!C now direction of gg_tube vector
+!C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
+ if (acavtub(iti).eq.0.0d0) then
+!C go to 667
+ enecavtube(i+nres)=0.0d0
+ faccav=0.0d0
+ else
+ denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6)
+ enecavtube(i+nres)= &
+ (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti)) &
+ /denominator
+!C enecavtube(i)=0.0
+ faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff)) &
+ *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff) &
+ +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0) &
+ /denominator**2.0d0
+!C faccav=0.0
+ fac=fac+faccav
+!C 667 continue
+ endif
+!C print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
+!C & enecavtube(i),faccav
+!C print *,"licz=",
+!C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+!C print *,"finene=",enetube(i+nres)+enecavtube(i)
+ do j=1,3
+ gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
+ gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
+ enddo
+ enddo
+
+
+
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i) &
+ +enecavtube(i+nres)
+ enddo
+!C print *,"ETUBE", etube
+ return
+ end subroutine calcnano
+
+!===============================================
!--------------------------------------------------------------------------------
!C first for shielding is setting of function of side-chains
allocate(gshieldc_ll(3,-1:nres))
allocate(gshieldc_loc_ll(3,-1:nres))
allocate(grad_shield(3,-1:nres))
+ allocate(gg_tube_sc(3,-1:nres))
+ allocate(gg_tube(3,-1:nres))
!(3,maxres)
allocate(grad_shield_side(3,50,nres))
allocate(grad_shield_loc(3,50,nres))
projects / unres4.git / blobdiff