From 7d64cc3ff0edffb6aa37e309e4375f58bd5875a2 Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Fri, 10 Mar 2017 11:01:50 +0100 Subject: [PATCH] Correction of D-AA to parmread --- source/unres/src_MD-M/energy_p_new_barrier.F | 89 +++- source/unres/src_MD-M/parmread.F | 28 +- source/wham/src-M/energy_p_new.F | 689 ++++++++++++++++++++++++++ 3 files changed, 788 insertions(+), 18 deletions(-) diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F index 91a7c94..a20ec7b 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -6329,6 +6329,9 @@ c else do j=1,nbi diff=vbld(i+nres)-vbldsc0(j,iti) + if (energy_dec) write (iout,*) + & "estr sc",i,iti,vbld(i+nres),vbldsc0(j,iti),diff, + & AKSC(j,iti),AKSC(j,iti)*diff*diff ud(j)=aksc(j,iti)*diff u(j)=abond0(j,iti)+0.5d0*ud(j)*diff enddo @@ -6662,6 +6665,7 @@ C etheta=0.0D0 do i=ithet_start,ithet_end c print *,i,itype(i-1),itype(i),itype(i-2) +C if (itype(i-1).eq.ntyp1) cycle if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 & .or.itype(i).eq.ntyp1) cycle C print *,i,theta(i) @@ -12337,10 +12341,31 @@ 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 +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) @@ -12359,14 +12384,61 @@ 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) + 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)=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)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6 + 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 + & 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 @@ -12375,6 +12447,11 @@ C now direction of gg_tube vector 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" diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F index 78d0afb..dc040cb 100644 --- a/source/unres/src_MD-M/parmread.F +++ b/source/unres/src_MD-M/parmread.F @@ -1038,22 +1038,26 @@ C write (iout,*) 'Type',i write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13) endif -c B1(1,i) = b(3) -c B1(2,i) = b(5) -c B1(1,-i) = b(3) -c B1(2,-i) = -b(5) + b(3,-i)= b(3,i) + b(5,-i)=-b(5,i) + b(4,-i)=-b(4,i) + b(2,-i)= b(2,i) + B1(1,i) = b(3,i) + B1(2,i) = b(5,i) + B1(1,-i) = b(3,i) + B1(2,-i) = -b(5,i) c b1(1,i)=0.0d0 c b1(2,i)=0.0d0 -c B1tilde(1,i) = b(3) -c B1tilde(2,i) =-b(5) -c B1tilde(1,-i) =-b(3) -c B1tilde(2,-i) =b(5) + B1tilde(1,i) = b(3,i) + B1tilde(2,i) =-b(5,i) + B1tilde(1,-i) =-b(3,i) + B1tilde(2,-i) =b(5,i) c b1tilde(1,i)=0.0d0 c b1tilde(2,i)=0.0d0 -c B2(1,i) = b(2) -c B2(2,i) = b(4) -c B2(1,-i) =b(2) -c B2(2,-i) =-b(4) + B2(1,i) = b(2,i) + B2(2,i) = b(4,i) + B2(1,-i) =b(2,i) + B2(2,-i) =-b(4,i) cc B1tilde(1,i) = b(3,i) cc B1tilde(2,i) =-b(5,i) C B1tilde(1,-i) =-b(3,i) diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F index b5f5705..6c943cc 100644 --- a/source/wham/src-M/energy_p_new.F +++ b/source/wham/src-M/energy_p_new.F @@ -9188,3 +9188,692 @@ C write(2,*) "TU",rpp(1,1),short,long,buff_shield return end +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) + 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=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 + 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 +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 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 +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----------------------------------------------------------------------- +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=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) + 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)=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) + 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=itube_start,itube_end + Etube=Etube+enetube(i)+enetube(i+nres) + 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 + + +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 calcnano(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), + & enecavtube(maxres*2) + 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 + xmin=boxxsize + ymin=boxysize + zmin=boxzsize + + 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 + vectube(3)=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + zminact=abs(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=(1.0+dcavtubpep*rdiff6*rdiff6) + enecavtube(i)= + & (bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)+ccavtubpep) + & /denominator + enecavtube(i)=0.0 + faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/sqrt(rdiff)) + & *denominator-(bcavtubpep*rdiff+acavtubpep*sqrt(rdiff) + & +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0) + & /denominator**2.0d0 +C faccav=0.0 +C fac=fac+faccav +C 667 continue + endif +C print *,"TUT",i,iti,rdiff,rdiff6,acavtubpep,denominator, +C & enecavtube(i),faccav +C print *,"licz=", +C & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) +CX print *,"finene=",enetube(i+nres)+enecavtube(i) + +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 + + do i=itube_start,itube_end + enecavtube(i)=0.0 +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)=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 + vectube(3)=mod((c(3,i+nres)),boxzsize) + vectube(3)=vectube(3)+boxzsize*j + + + xminact=abs(vectube(1)-tubecenter(1)) + yminact=abs(vectube(2)-tubecenter(2)) + zminact=abs(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 +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 +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)=0.0 + faccav=0.0 + else + denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6) + enecavtube(i+nres)= + & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) + & /denominator +C enecavtube(i)=0.0 + faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/sqrt(rdiff)) + & *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*sqrt(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 +C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12) +C do i=itube_start,itube_end +C enecav(i)=0.0 +C iti=itype(i) +C if (acavtub(iti).eq.0.0) cycle + + + + 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 +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 + -- 1.7.9.5