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=a20ec7bbfb800a20525e2cfcd44bc169ba5a81c2;hb=7d64cc3ff0edffb6aa37e309e4375f58bd5875a2;hp=c037ff398718f15b45003050c68b7aef0c2cecc7;hpb=4d4be87fb43102a6a5be442699a953ef327ecbde;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 c037ff3..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" @@ -12589,7 +12666,30 @@ C now we calculate gradient & 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 @@ -12669,11 +12769,11 @@ 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)=0.0 + enecavtube(i+nres)=0.0 faccav=0.0 else denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6) - enecavtube(i)= + enecavtube(i+nres)= & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) & /denominator C enecavtube(i)=0.0 @@ -12685,11 +12785,11 @@ C faccav=0.0 fac=fac+faccav C 667 continue endif - print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator, - & enecavtube(i),faccav - print *,"licz=", - & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti)) - print *,"finene=",enetube(i+nres)+enecavtube(i) +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 @@ -12705,6 +12805,7 @@ 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