X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Fenergy_p_new_barrier.F;h=f557ebccc9e2f2bc50b187bfec041003932498fd;hb=14b55af23c7da34bfdc10f315551c8e01a3a906a;hp=e86bb6e5de8c25d35efb9c03e5eb07ea42b73499;hpb=c1827efa66e69c93c6e2b2e7420b06b430c3550a;p=unres.git 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 e86bb6e..f557ebc 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -307,9 +307,11 @@ C print *,"za lipidami" 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 @@ -11534,7 +11536,8 @@ C the vector between center of side_chain and peptide group &pept_group(3),costhet_grad(3),cosphi_grad_long(3), &cosphi_grad_loc(3),pep_side_norm(3),side_calf_norm(3) C the line belowe needs to be changed for FGPROC>1 - do i=1,nres-1 + do i=iatscp_s,iatscp_e +C do i=1,nres-1 if ((itype(i).eq.ntyp1).and.itype(i+1).eq.ntyp1) cycle ishield_list(i)=0 Cif there two consequtive dummy atoms there is no peptide group between them @@ -11725,8 +11728,13 @@ C for UNRES 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) @@ -11768,8 +11776,15 @@ C lets ommit dummy atoms for now 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 @@ -11810,3 +11825,189 @@ 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=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 +