#ifdef MPI
include "mpif.h"
double precision weights_(n_ene)
+ integer IERR
+ integer status(MPI_STATUS_SIZE)
#endif
include 'COMMON.SETUP'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.TIME1'
include 'COMMON.SPLITELE'
+ include 'COMMON.SHIELD'
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
call set_shield_fac
else if (shield_mode.eq.2) then
call set_shield_fac2
+ if (nfgtasks.gt.1) then
+C#define DEBUG
+#ifdef DEBUG
+ write(iout,*) "befor reduce fac_shield reduce"
+ do i=1,nres
+ write(2,*) "fac",itype(i),fac_shield(i),grad_shield(1,i)
+ write(2,*) "list", shield_list(1,i),ishield_list(i),
+ & grad_shield_side(1,1,i),grad_shield_loc(1,1,i)
+ enddo
+#endif
+ call MPI_Allgatherv(fac_shield(ivec_start),ivec_count(fg_rank1),
+ & MPI_DOUBLE_PRECISION,fac_shield(1),ivec_count(0),ivec_displ(0),
+ & MPI_DOUBLE_PRECISION,FG_COMM,IERR)
+ call MPI_Allgatherv(shield_list(1,ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_I50,shield_list(1,1),ivec_count(0),
+ & ivec_displ(0),
+ & MPI_I50,FG_COMM,IERR)
+ call MPI_Allgatherv(ishield_list(ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_INTEGER,ishield_list(1),ivec_count(0),
+ & ivec_displ(0),
+ & MPI_INTEGER,FG_COMM,IERR)
+ call MPI_Allgatherv(grad_shield(1,ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_UYZ,grad_shield(1,1),ivec_count(0),
+ & ivec_displ(0),
+ & MPI_UYZ,FG_COMM,IERR)
+ call MPI_Allgatherv(grad_shield_side(1,1,ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_SHI,grad_shield_side(1,1,1),ivec_count(0),
+ & ivec_displ(0),
+ & MPI_SHI,FG_COMM,IERR)
+ call MPI_Allgatherv(grad_shield_loc(1,1,ivec_start),
+ & ivec_count(fg_rank1),
+ & MPI_SHI,grad_shield_loc(1,1,1),ivec_count(0),
+ & ivec_displ(0),
+ & MPI_SHI,FG_COMM,IERR)
+#ifdef DEBUG
+ write(iout,*) "after reduce fac_shield reduce"
+ do i=1,nres
+ write(2,*) "fac",itype(i),fac_shield(i),grad_shield(1,i)
+ write(2,*) "list", shield_list(1,i),ishield_list(i),
+ & grad_shield_side(1,1,i),grad_shield_loc(1,1,i)
+ enddo
+#endif
+C#undef DEBUG
+ endif
+#ifdef DEBUG
+ do i=1,nres
+ write(iout,*) fac_shield(i),ishield_list(i),i,grad_shield(1,i)
+ do j=1,ishield_list(i)
+ write(iout,*) "grad", grad_shield_side(1,j,i),
+ & grad_shield_loc(1,j,i)
+ enddo
+ enddo
+#endif
endif
c print *,"Processor",myrank," left VEC_AND_DERIV"
if (ipot.lt.6) then
C print *,"przed lipidami"
if (wliptran.gt.0) then
call Eliptransfer(eliptran)
+ else
+ eliptran=0.0d0
endif
C print *,"za lipidami"
if (AFMlog.gt.0) then
else if (selfguide.gt.0) then
call AFMvel(Eafmforce)
endif
- if (TUBElog.gt.0) then
+ if (TUBElog.eq.1) then
C print *,"just before call"
call calctube(Etube)
+ elseif (TUBElog.eq.2) then
+ call calctube2(Etube)
else
Etube=0.0d0
endif
time00=MPI_Wtime()
call MPI_Reduce(enebuff(0),energia(0),n_ene+1,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
-#ifdef DEBUG
+C#ifdef DEBUG
write (iout,*) "energies after REDUCE"
call enerprint(energia)
call flush(iout)
-#endif
+C#endif
time_Reduce=time_Reduce+MPI_Wtime()-time00
endif
if (fg_rank.eq.0) then
C fac_shield(i)=0.4
C fac_shield(j)=0.6
endif
+C if (j.eq.78)
+C & write(iout,*) i,j,fac_shield(i),fac_shield(j)
eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
-C#ifdef NEWCORR
+#ifdef NEWCORR
C Derivatives in theta
gloc(nphi+i,icg)=gloc(nphi+i,icg)
& +0.5d0*(gpizda1(1,1)+gpizda1(2,2))*wturn3
gloc(nphi+i+1,icg)=gloc(nphi+i+1,icg)
& +0.5d0*(gpizda2(1,1)+gpizda2(2,2))*wturn3
& *fac_shield(i)*fac_shield(j)
-C#endif
+#endif
C if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
C Derivatives in shield mode
include 'COMMON.IOUNITS'
include 'COMMON.SHIELD'
include 'COMMON.INTERACT'
+ include 'COMMON.LOCAL'
+
C this is the squar root 77 devided by 81 the epislion in lipid (in protein)
double precision div77_81/0.974996043d0/,
&div4_81/0.2222222222d0/,sh_frac_dist_grad(3)
-
+
C the vector between center of side_chain and peptide group
double precision pep_side(3),long,side_calf(3),
&pept_group(3),costhet_grad(3),cosphi_grad_long(3),
&cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3)
+C write(2,*) "ivec",ivec_start,ivec_end
+ do i=1,nres
+ fac_shield(i)=0.0d0
+ do j=1,3
+ grad_shield(j,i)=0.0d0
+ enddo
+ enddo
C the line belowe needs to be changed for FGPROC>1
- do i=1,nres-1
- if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
+ do i=ivec_start,ivec_end
+C do i=1,nres-1
+C if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
ishield_list(i)=0
+ if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle
Cif there two consequtive dummy atoms there is no peptide group between them
C the line below has to be changed for FGPROC>1
VolumeTotal=0.0
C print *,buff_shield,"buff"
C now sscale
if (sh_frac_dist.le.0.0) cycle
+C print *,ishield_list(i),i
C If we reach here it means that this side chain reaches the shielding sphere
C Lets add him to the list for gradient
ishield_list(i)=ishield_list(i)+1
VolumeTotal=VolumeTotal+VofOverlap*scale_fac_dist
enddo
fac_shield(i)=VolumeTotal*wshield+(1.0d0-wshield)
-C write(2,*) "TOTAL VOLUME",i,VolumeTotal,fac_shield(i)
+C write(2,*) "TOTAL VOLUME",i,itype(i),fac_shield(i)
enddo
return
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
- vectube(1)=(c(1,i)+c(1,i+1))/2.0d0-tubecenter(1)
- vectube(2)=(c(2,i)+c(2,i+1))/2.0d0-tubecenter(2)
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ 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 in UNRES uncomment the line below as GLY has no side-chain...
C .or.(iti.eq.10)
& ) cycle
- vectube(1)=c(1,i+nres)-tubecenter(1)
- vectube(2)=c(2,i+nres)-tubecenter(2)
+ 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 as the tube is infinity we do not calculate the Z-vector use of Z
C as chosen axis
C 5) add COMMONs
C 6) add to zerograd
+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)
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+ include 'COMMON.GEO'
+ include 'COMMON.VAR'
+ include 'COMMON.LOCAL'
+ include 'COMMON.CHAIN'
+ include 'COMMON.DERIV'
+ include 'COMMON.NAMES'
+ include 'COMMON.INTERACT'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.CALC'
+ include 'COMMON.CONTROL'
+ include 'COMMON.SPLITELE'
+ include 'COMMON.SBRIDGE'
+ double precision tub_r,vectube(3),enetube(maxres*2)
+ Etube=0.0d0
+ do i=1,2*nres
+ enetube(i)=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=1,nres
+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
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ 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)
+ do i=1,nres
+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)
+ 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
+ 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=1,2*nres
+ Etube=Etube+enetube(i)
+ enddo
+C print *,"ETUBE", etube
+ return
+ end
+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
+