X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fwham%2Fsrc-M%2Fenergy_p_new.F;h=6c943cc99396daa921b2d998324174e3d9a84585;hb=7d64cc3ff0edffb6aa37e309e4375f58bd5875a2;hp=fb18913435cc4daf46f956bdf7c2a19b66cf1132;hpb=48f04f24e913a3e10867d2038b30efcd48a60a9f;p=unres.git diff --git a/source/wham/src-M/energy_p_new.F b/source/wham/src-M/energy_p_new.F index fb18913..6c943cc 100644 --- a/source/wham/src-M/energy_p_new.F +++ b/source/wham/src-M/energy_p_new.F @@ -250,11 +250,28 @@ C & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(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) + gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(2)*gsccorx(j,i) & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + else gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i) & +fact(1)*wscp*gvdwc_scp(j,i)+ @@ -312,11 +329,28 @@ C & wturn6*fact(5)*gcorr6_turn(j,i)+ & wsccor*fact(2)*gsccorc(j,i) & +wliptran*gliptranc(j,i) + & +welec*gshieldc(j,i) + & +welec*gshieldc_loc(j,i) + & +wcorr*gshieldc_ec(j,i) + & +wcorr*gshieldc_loc_ec(j,i) + & +wturn3*gshieldc_t3(j,i) + & +wturn3*gshieldc_loc_t3(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) + gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+ & wbond*gradbx(j,i)+ & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+ & wsccor*fact(1)*gsccorx(j,i) & +wliptran*gliptranx(j,i) + & +welec*gshieldx(j,i) + & +wcorr*gshieldx_ec(j,i) + & +wturn3*gshieldx_t3(j,i) + & +wturn4*gshieldx_t4(j,i) + & +wel_loc*gshieldx_ll(j,i) + else gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)+ & fact(1)*wscp*gvdwc_scp(j,i)+ @@ -2171,10 +2205,35 @@ C endif if (ymedi.lt.0) ymedi=ymedi+boxysize zmedi=mod(zmedi,boxzsize) if (zmedi.lt.0) zmedi=zmedi+boxzsize + zmedi2=mod(zmedi,boxzsize) + if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize + if ((zmedi2.gt.bordlipbot) + &.and.(zmedi2.lt.bordliptop)) then +C the energy transfer exist + if (zmedi2.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zmedi2-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipi=sscalelip(fracinbuf) + ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick + elseif (zmedi2.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick) + sslipi=sscalelip(fracinbuf) + ssgradlipi=sscagradlip(fracinbuf)/lipbufthick + else + sslipi=1.0d0 + ssgradlipi=0.0d0 + endif + else + sslipi=0.0d0 + ssgradlipi=0.0d0 + endif + num_conti=0 C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i) do j=ielstart(i),ielend(i) - if (j.le.1) cycle + if (j.lt.1) cycle C if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1 C & .or.itype(j+2).eq.ntyp1 C &) cycle @@ -2216,6 +2275,28 @@ C End diagnostics if (yj.lt.0) yj=yj+boxysize zj=mod(zj,boxzsize) if (zj.lt.0) zj=zj+boxzsize + if ((zj.gt.bordlipbot) + &.and.(zj.lt.bordliptop)) then +C the energy transfer exist + if (zj.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zj-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zj.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) + sslipj=sscalelip(fracinbuf) + ssgradlipj=sscagradlip(fracinbuf)/lipbufthick + else + sslipj=1.0d0 + ssgradlipj=0.0 + endif + else + sslipj=0.0d0 + ssgradlipj=0.0 + endif dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2 xj_safe=xj yj_safe=yj @@ -2722,6 +2803,7 @@ C fac_shield(j)=0.6 endif eel_loc_ij=eel_loc_ij & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij C write (iout,'(a6,2i5,0pf7.3)') C & 'eelloc',i,j,eel_loc_ij @@ -2779,11 +2861,13 @@ C Partial derivatives in virtual-bond dihedral angles gamma & (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j) & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc_loc(j-1)=gel_loc_loc(j-1)+ & (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j) & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij) cd write(iout,*) 'agg ',agg @@ -2797,6 +2881,7 @@ C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2) ggg(l)=(agg(l,1)*muij(1)+ & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo do k=i+2,j2 @@ -2809,18 +2894,22 @@ C Remaining derivatives of eello gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+ & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+ & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+ & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+ & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo endif @@ -3083,6 +3172,37 @@ C Third- and fourth-order contributions from turns double precision agg(3,4),aggi(3,4),aggi1(3,4), & aggj(3,4),aggj1(3,4),a_temp(2,2) common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2 + zj=(c(3,j)+c(3,j+1))/2.0d0 +C xj=mod(xj,boxxsize) +C if (xj.lt.0) xj=xj+boxxsize +C yj=mod(yj,boxysize) +C if (yj.lt.0) yj=yj+boxysize + zj=mod(zj,boxzsize) + if (zj.lt.0) zj=zj+boxzsize +C if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ" + if ((zj.gt.bordlipbot) + &.and.(zj.lt.bordliptop)) then +C the energy transfer exist + if (zj.lt.buflipbot) then +C what fraction I am in + fracinbuf=1.0d0- + & ((zj-bordlipbot)/lipbufthick) +C lipbufthick is thickenes of lipid buffore + sslipj=sscalelip(fracinbuf) + ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick + elseif (zj.gt.bufliptop) then + fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick) + sslipj=sscalelip(fracinbuf) + ssgradlipj=sscagradlip(fracinbuf)/lipbufthick + else + sslipj=1.0d0 + ssgradlipj=0.0 + endif + else + sslipj=0.0d0 + ssgradlipj=0.0 + endif + if (j.eq.i+2) then if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds @@ -3120,8 +3240,11 @@ C fac_shield(j)=0.6 eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + eello_t3=0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) cd write (2,*) 'i,',i,' j',j,'eello_turn3', cd & 0.5d0*(pizda(1,1)+pizda(2,2)), @@ -3176,6 +3299,8 @@ C Derivatives in gamma(i) call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1)) gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) + C Derivatives in gamma(i+1) call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1)) call transpose2(auxmat2(1,1),pizda(1,1)) @@ -3183,6 +3308,7 @@ C Derivatives in gamma(i+1) gel_loc_turn3(i+1)=gel_loc_turn3(i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) C Cartesian derivatives do l=1,3 @@ -3194,6 +3320,7 @@ C Cartesian derivatives gcorr3_turn(l,i)=gcorr3_turn(l,i) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) @@ -3203,6 +3330,7 @@ C Cartesian derivatives gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) @@ -3212,6 +3340,7 @@ C Cartesian derivatives gcorr3_turn(l,j)=gcorr3_turn(l,j) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) @@ -3221,6 +3350,7 @@ C Cartesian derivatives gcorr3_turn(l,j1)=gcorr3_turn(l,j1) & +0.5d0*(pizda(1,1)+pizda(2,2)) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo endif @@ -3330,6 +3460,7 @@ C & *2.0 s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) C Derivatives in gamma(i+1) call transpose2(EUgder(1,1,i+2),e2tder(1,1)) @@ -3340,6 +3471,7 @@ C Derivatives in gamma(i+1) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) C Derivatives in gamma(i+2) call transpose2(EUgder(1,1,i+3),e3tder(1,1)) @@ -3353,6 +3485,7 @@ C Derivatives in gamma(i+2) s3=0.5d0*(pizda(1,1)+pizda(2,2)) gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) C Cartesian derivatives @@ -3375,6 +3508,7 @@ C Derivatives of this turn contributions in DC(i+2) ggg(l)=-(s1+s2+s3) gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo endif @@ -3395,6 +3529,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggi1(l,1) a_temp(1,2)=aggi1(l,2) @@ -3411,6 +3546,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggj(l,1) a_temp(1,2)=aggj(l,2) @@ -3427,6 +3563,7 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) a_temp(1,1)=aggj1(l,1) a_temp(1,2)=aggj1(l,2) @@ -3443,8 +3580,17 @@ C Remaining derivatives of this turn contribution s3=0.5d0*(pizda(1,1)+pizda(2,2)) gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3) & *fac_shield(i)*fac_shield(j) + &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0) enddo + gshieldc_t4(3,i)=gshieldc_t4(3,i)+ + & ssgradlipi*eello_t4/4.0d0*lipscale + gshieldc_t4(3,j)=gshieldc_t4(3,j)+ + & ssgradlipj*eello_t4/4.0d0*lipscale + gshieldc_t4(3,i-1)=gshieldc_t4(3,i-1)+ + & ssgradlipi*eello_t4/4.0d0*lipscale + gshieldc_t4(3,j-1)=gshieldc_t4(3,j-1)+ + & ssgradlipj*eello_t4/4.0d0*lipscale endif 178 continue endif @@ -9042,3 +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 +