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=8a2d03521e0266efe1ef6f34420ffb337bee2c47;hb=00ff2d632b212c4d4a388e8f7f5394763b65e3bb;hp=8fdffe3b05a3697357cc22f8b838c1d4037a4127;hpb=aedd2f72960d9cec69fcc7f0b6fd6555c7e22312;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 8fdffe3..8a2d035 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -142,8 +142,10 @@ C the shielding factor is set this factor is describing how each C peptide group is shielded by side-chains C the matrix - shield_fac(i) the i index describe the ith between i and i+1 C write (iout,*) "shield_mode",shield_mode - if (shield_mode.gt.0) then + if (shield_mode.eq.1) then call set_shield_fac + else if (shield_mode.eq.2) then + call set_shield_fac2 endif c print *,"Processor",myrank," left VEC_AND_DERIV" if (ipot.lt.6) then @@ -224,6 +226,7 @@ C C Calculate the virtual-bond torsional energy. C cd print *,'nterm=',nterm +C print *,"tor",tor_mode if (wtor.gt.0) then if ((tor_mode.eq.0).or.(tor_mode.eq.2)) then call etor(etors,edihcnstr) @@ -231,7 +234,7 @@ cd print *,'nterm=',nterm C etor kcc is Kubo cumulant clustered rigorous attemp to derive the C energy function if ((tor_mode.eq.1).or.(tor_mode.eq.2)) then - call etor(etors,edihcnstr) + call etor_kcc(etors,edihcnstr) endif else etors=0 @@ -1003,6 +1006,7 @@ c------------------------------------------------------------------------------- include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.SBRIDGE' + include 'COMMON.CONTROL' double precision kfac /2.4d0/ double precision x,x2,x3,x4,x5,licznik /1.12692801104297249644/ c facT=temp0/t_bath @@ -1038,6 +1042,11 @@ c facT=2*temp0/(t_bath+temp0) #endif stop 555 endif + if (shield_mode.gt.0) then + wscp=weights(2)*fact + wsc=weights(1)*fact + wvdwpp=weights(16)*fact + endif welec=weights(3)*fact wcorr=weights(4)*fact3 wcorr5=weights(5)*fact4 @@ -2774,28 +2783,28 @@ c write(iout,*) 'nphi=',nphi,nres #endif #ifdef NEWCORR if (i.gt. nnt+2 .and. i.lt.nct+2) then - iti = itortyp(itype(i-2)) + iti = itype2loc(itype(i-2)) else - iti=ntortyp+1 + iti=nloctyp endif c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp+1 + iti1=nloctyp endif c write(iout,*),i - b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0) + b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0d0) & +bnew1(2,1,iti)*dsin(theta(i-1)) - & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0) + & +bnew1(3,1,iti)*dcos(theta(i-1)/2.0d0) gtb1(1,i-2)=bnew1(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0 & +bnew1(2,1,iti)*dcos(theta(i-1)) & -bnew1(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0 c & +bnew1(3,1,iti)*sin(alpha(i))*cos(beta(i)) c &*(cos(theta(i)/2.0) - b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0) + b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0d0) & +bnew2(2,1,iti)*dsin(theta(i-1)) - & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0) + & +bnew2(3,1,iti)*dcos(theta(i-1)/2.0d0) c & +bnew2(3,1,iti)*sin(alpha(i))*cos(beta(i)) c &*(cos(theta(i)/2.0) gtb2(1,i-2)=bnew2(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0 @@ -2834,15 +2843,15 @@ c write (iout,*) 'theta=', theta(i-1) enddo #else if (i.gt. nnt+2 .and. i.lt.nct+2) then - iti = itortyp(itype(i-2)) + iti = itype2loc(itype(i-2)) else - iti=ntortyp+1 + iti=nloctyp endif c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp+1 + iti1=nloctyp endif b1(1,i-2)=b(3,iti) b1(2,i-2)=b(5,iti) @@ -2931,15 +2940,15 @@ c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then endif c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then if (i.gt. nnt+2 .and. i.lt.nct+2) then - iti = itortyp(itype(i-2)) + iti = itype2loc(itype(i-2)) else - iti=ntortyp + iti=nloctyp endif c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp + iti1=nloctyp endif cd write (iout,*) '*******i',i,' iti1',iti cd write (iout,*) 'b1',b1(:,iti) @@ -2952,8 +2961,8 @@ c if (i .gt. iatel_s+2) then call matvec2(Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2)) c write (iout,*) Ug(1,1,i-2),gtb2(1,i-2),gUb2(1,i-2),"chuj" #endif -c write(iout,*) "co jest kurwa", iti, EE(1,1,iti),EE(2,1,iti), -c & EE(1,2,iti),EE(2,2,iti) +c write(iout,*) "co jest kurwa", iti, EE(1,1,i),EE(2,1,i), +c & EE(1,2,iti),EE(2,2,i) call matmat2(EE(1,1,i-2),Ug(1,1,i-2),EUg(1,1,i-2)) call matmat2(gtEE(1,1,i-2),Ug(1,1,i-2),gtEUg(1,1,i-2)) c write(iout,*) "Macierz EUG", @@ -2988,18 +2997,24 @@ c & eug(2,2,i-2) c if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then if (i.gt. nnt+1 .and. i.lt.nct+1) then if (itype(i-1).le.ntyp) then - iti1 = itortyp(itype(i-1)) + iti1 = itype2loc(itype(i-1)) else - iti1=ntortyp + iti1=nloctyp endif else - iti1=ntortyp + iti1=nloctyp endif do k=1,2 mu(k,i-2)=Ub2(k,i-2)+b1(k,i-1) enddo -C write (iout,*) 'mumu',i,b1(1,i-1),Ub2(1,i-2) -c write (iout,*) 'mu ',mu(:,i-2),i-2 +#ifdef MUOUT + write (iout,'(2hmu,i3,3f8.1,12f10.5)') i-2,rad2deg*theta(i-1), + & rad2deg*theta(i),rad2deg*phi(i),mu(1,i-2),mu(2,i-2), + & -b2(1,i-2),b2(2,i-2),b1(1,i-2),b1(2,i-2), + & dsqrt(b2(1,i-1)**2+b2(2,i-1)**2) + & +dsqrt(b1(1,i-1)**2+b1(2,i-1)**2), + & ((ee(l,k,i-2),l=1,2),k=1,2),eenew(1,itype2loc(iti)) +#endif cd write (iout,*) 'mu1',mu1(:,i-2) cd write (iout,*) 'mu2',mu2(:,i-2) if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.wcorr6.gt.0.0d0) @@ -3286,11 +3301,11 @@ c endif #endif #endif cd do i=1,nres -cd iti = itortyp(itype(i)) +cd iti = itype2loc(itype(i)) cd write (iout,*) i cd do j=1,2 cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)') -cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2) +cd & (EE(j,k,i),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2) cd enddo cd enddo return @@ -3408,21 +3423,23 @@ C Loop over i,i+2 and i,i+3 pairs of the peptide groups C C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition do i=iturn3_start,iturn3_end - if (i.le.1) cycle +c if (i.le.1) cycle C write(iout,*) "tu jest i",i if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds - & .or.((i+4).gt.nres) - & .or.((i-1).le.0) +C Adam: Unnecessary: handled by iturn3_end and iturn3_start +c & .or.((i+4).gt.nres) +c & .or.((i-1).le.0) C end of changes by Ana & .or. itype(i+2).eq.ntyp1 & .or. itype(i+3).eq.ntyp1) cycle - if(i.gt.1)then - if(itype(i-1).eq.ntyp1)cycle - end if - if(i.LT.nres-3)then - if (itype(i+4).eq.ntyp1) cycle - end if +C Adam: Instructions below will switch off existing interactions +c if(i.gt.1)then +c if(itype(i-1).eq.ntyp1)cycle +c end if +c if(i.LT.nres-3)then +c if (itype(i+4).eq.ntyp1) cycle +c end if dxi=dc(1,i) dyi=dc(2,i) dzi=dc(3,i) @@ -3447,14 +3464,14 @@ C end of changes by Ana if (i.le.1) cycle if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds - & .or.((i+5).gt.nres) - & .or.((i-1).le.0) +c & .or.((i+5).gt.nres) +c & .or.((i-1).le.0) C end of changes suggested by Ana & .or. itype(i+3).eq.ntyp1 & .or. itype(i+4).eq.ntyp1 - & .or. itype(i+5).eq.ntyp1 - & .or. itype(i).eq.ntyp1 - & .or. itype(i-1).eq.ntyp1 +c & .or. itype(i+5).eq.ntyp1 +c & .or. itype(i).eq.ntyp1 +c & .or. itype(i-1).eq.ntyp1 & ) cycle dxi=dc(1,i) dyi=dc(2,i) @@ -3514,14 +3531,14 @@ c CTU KURWA do i=iatel_s,iatel_e C do i=75,75 - if (i.le.1) cycle +c if (i.le.1) cycle if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds - & .or.((i+2).gt.nres) - & .or.((i-1).le.0) +c & .or.((i+2).gt.nres) +c & .or.((i-1).le.0) C end of changes by Ana - & .or. itype(i+2).eq.ntyp1 - & .or. itype(i-1).eq.ntyp1 +c & .or. itype(i+2).eq.ntyp1 +c & .or. itype(i-1).eq.ntyp1 & ) cycle dxi=dc(1,i) dyi=dc(2,i) @@ -3577,11 +3594,11 @@ C write (iout,*) i,j if (j.le.1) cycle if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1 C changes suggested by Ana to avoid out of bounds - & .or.((j+2).gt.nres) - & .or.((j-1).le.0) +c & .or.((j+2).gt.nres) +c & .or.((j-1).le.0) C end of changes by Ana - & .or.itype(j+2).eq.ntyp1 - & .or.itype(j-1).eq.ntyp1 +c & .or.itype(j+2).eq.ntyp1 +c & .or.itype(j-1).eq.ntyp1 &) cycle call eelecij(i,j,ees,evdw1,eel_loc) enddo ! j @@ -4823,9 +4840,9 @@ c write(iout,*)"WCHODZE W PROGRAM" a_temp(1,2)=a23 a_temp(2,1)=a32 a_temp(2,2)=a33 - iti1=itortyp(itype(i+1)) - iti2=itortyp(itype(i+2)) - iti3=itortyp(itype(i+3)) + iti1=itype2loc(itype(i+1)) + iti2=itype2loc(itype(i+2)) + iti3=itype2loc(itype(i+3)) c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3 call transpose2(EUg(1,1,i+1),e1t(1,1)) call transpose2(Eug(1,1,i+2),e2t(1,1)) @@ -7464,11 +7481,15 @@ C The rigorous attempt to derive energy function include 'COMMON.TORCNSTR' include 'COMMON.CONTROL' logical lprn - double precision thybt1(maxtermkcc),thybt2(maxtermkcc) +c double precision thybt1(maxtermkcc),thybt2(maxtermkcc) C Set lprn=.true. for debugging lprn=.false. c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "etor_kcc tor_mode",tor_mode + if (tor_mode.ne.2) then etors=0.0D0 + endif do i=iphi_start,iphi_end C ANY TWO ARE DUMMY ATOMS in row CYCLE c if (((itype(i-3).eq.ntyp1).and.(itype(i-2).eq.ntyp1)).or. @@ -7485,74 +7506,106 @@ c & ((itype(i-1).eq.ntyp1).and.(itype(i).eq.ntyp1))) cycle sumnonchebyshev=0.0d0 sumchebyshev=0.0d0 C to avoid multiple devision by 2 - theti22=0.5d0*theta(i) +c theti22=0.5d0*theta(i) C theta 12 is the theta_1 /2 C theta 22 is theta_2 /2 - theti12=0.5d0*theta(i-1) +c theti12=0.5d0*theta(i-1) C and appropriate sinus function - sinthet2=dsin(theta(i)) sinthet1=dsin(theta(i-1)) + sinthet2=dsin(theta(i)) costhet1=dcos(theta(i-1)) costhet2=dcos(theta(i)) +c Cosines of halves thetas + costheti12=0.5d0*(1.0d0+costhet1) + costheti22=0.5d0*(1.0d0+costhet2) C to speed up lets store its mutliplication - sint1t2=sinthet2*sinthet1 + sint1t2=sinthet2*sinthet1 + sint1t2n=1.0d0 C \sum_{i=1}^n (sin(theta_1) * sin(theta_2))^n * (c_n* cos(n*gamma) C +d_n*sin(n*gamma)) * C \sum_{i=1}^m (1+a_m*Tb_m(cos(theta_1 /2))+b_m*Tb_m(cos(theta_2 /2))) C we have two sum 1) Non-Chebyshev which is with n and gamma + etori=0.0d0 do j=1,nterm_kcc(itori,itori1) + nval=nterm_kcc_Tb(itori,itori1) v1ij=v1_kcc(j,itori,itori1) v2ij=v2_kcc(j,itori,itori1) +c write (iout,*) "i",i," j",j," v1",v1ij," v2",v2ij C v1ij is c_n and d_n in euation above cosphi=dcos(j*phii) sinphi=dsin(j*phii) - sint1t2n=sint1t2**j - sumnonchebyshev=sumnonchebyshev+ - & sint1t2n*(v1ij*cosphi+v2ij*sinphi) - actval=sint1t2n*(v1ij*cosphi+v2ij*sinphi) + sint1t2n1=sint1t2n + sint1t2n=sint1t2n*sint1t2 + sumth1tyb1=tschebyshev(1,nval,v11_chyb(1,j,itori,itori1), + & costheti12) + gradth1tyb1=-0.5d0*sinthet1*gradtschebyshev(0,nval-1, + & v11_chyb(1,j,itori,itori1),costheti12) +c write (iout,*) "v11",(v11_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth1tyb1",sumth1tyb1," gradth1tyb1",gradth1tyb1 + sumth2tyb1=tschebyshev(1,nval,v21_chyb(1,j,itori,itori1), + & costheti22) + gradth2tyb1=-0.5d0*sinthet2*gradtschebyshev(0,nval-1, + & v21_chyb(1,j,itori,itori1),costheti22) +c write (iout,*) "v21",(v21_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth2tyb1",sumth2tyb1," gradth2tyb1",gradth2tyb1 + sumth1tyb2=tschebyshev(1,nval,v12_chyb(1,j,itori,itori1), + & costheti12) + gradth1tyb2=-0.5d0*sinthet1*gradtschebyshev(0,nval-1, + & v12_chyb(1,j,itori,itori1),costheti12) +c write (iout,*) "v12",(v12_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth1tyb2",sumth1tyb2," gradth1tyb2",gradth1tyb2 + sumth2tyb2=tschebyshev(1,nval,v22_chyb(1,j,itori,itori1), + & costheti22) + gradth2tyb2=-0.5d0*sinthet2*gradtschebyshev(0,nval-1, + & v22_chyb(1,j,itori,itori1),costheti22) +c write (iout,*) "v22",(v22_chyb(k,j,itori,itori1),k=1,nval), +c & " sumth2tyb2",sumth2tyb2," gradth2tyb2",gradth2tyb2 C etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi) C if (energy_dec) etors_ii=etors_ii+ C & v1ij*cosphi+v2ij*sinphi C glocig is the gradient local i site in gamma - glocig=glocig+j*(v2ij*cosphi-v1ij*sinphi)*sint1t2n + actval1=v1ij*cosphi*(1.0d0+sumth1tyb1+sumth2tyb1) + actval2=v2ij*sinphi*(1.0d0+sumth1tyb2+sumth2tyb2) + etori=etori+sint1t2n*(actval1+actval2) + glocig=glocig+ + & j*sint1t2n*(v2ij*cosphi*(1.0d0+sumth1tyb2+sumth2tyb2) + & -v1ij*sinphi*(1.0d0+sumth1tyb1+sumth2tyb1)) C now gradient over theta_1 - glocit1=glocit1+actval/sinthet1*j*costhet1 - glocit2=glocit2+actval/sinthet2*j*costhet2 - enddo + glocit1=glocit1+ + & j*sint1t2n1*costhet1*sinthet2*(actval1+actval2)+ + & sint1t2n*(v1ij*cosphi*gradth1tyb1+v2ij*sinphi*gradth1tyb2) + glocit2=glocit2+ + & j*sint1t2n1*sinthet1*costhet2*(actval1+actval2)+ + & sint1t2n*(v1ij*cosphi*gradth2tyb1+v2ij*sinphi*gradth2tyb2) C now the Czebyshev polinominal sum - do j=1,nterm_kcc_Tb(itori,itori1) - thybt1(j)=v1_chyb(j,itori,itori1) - thybt2(j)=v2_chyb(j,itori,itori1) - enddo - sumth1thyb=tschebyshev - & (1,nterm_kcc_Tb(itori,itori1),thybt1(1),dcos(theta12)) - gradthybt1=gradtschebyshev - & (0,nterm_kcc_Tb(itori,itori1)-1,thybt1(1),dcos(theta12)) - & *(nterm_kcc_Tb(itori,itori1))*0.5*dsin(theta12) - sumth2thyb=tschebyshev - & (1,nterm_kcc_Tb(itori,itori1),thybt2(1),dcos(theta22)) - gradthybt2=gradtschebyshev - & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),dcos(theta22)) - & *(nterm_kcc_Tb(itori,itori1))*0.5*dsin(theta22) +c do k=1,nterm_kcc_Tb(itori,itori1) +c thybt1(k)=v1_chyb(k,j,itori,itori1) +c thybt2(k)=v2_chyb(k,j,itori,itori1) +C thybt1(k)=0.0 +C thybt2(k)=0.0 +c enddo +C print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2, +C & gradtschebyshev +C & (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1), +C & dcos(theti22)**2), +C & dsin(theti22) C now overal sumation - etors=etors+(1.0d0+sumth1thyb+sumth2thyb)*sumnonchebyshev +C print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb + enddo ! j + etors=etors+etori C derivative over gamma - gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig - & *(1.0d0+sumth1thyb+sumth2thyb) + gloc(i-3,icg)=gloc(i-3,icg)+wtor*glocig C derivative over theta1 - gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wang* - & (glocit1*(1.0d0+sumth1thyb+sumth2thyb)+ - & sumnonchebyshev*gradthybt1) + gloc(nphi+i-3,icg)=gloc(nphi+i-3,icg)+wtor*glocit1 C now derivative over theta2 - gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang* - & (glocit2*(1.0d0+sumth1thyb+sumth2thyb)+ - & sumnonchebyshev*gradthybt2) - enddo - - + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wtor*glocit2 + if (lprn) + & write (iout,*) i-2,i-1,itype(i-2),itype(i-1),itori,itori1, + & theta(i-1)*rad2deg,theta(i)*rad2deg,phii*rad2deg,etori + enddo C gloc(i-3,icg)=gloc(i-3,icg)+wtor*gloci ! 6/20/98 - dihedral angle constraints if (tor_mode.ne.2) then @@ -7578,8 +7631,84 @@ c do i=1,ndih_constr return end +C The rigorous attempt to derive energy function + subroutine ebend_kcc(etheta,ethetacnstr) - + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.VAR' + include 'COMMON.GEO' + include 'COMMON.LOCAL' + include 'COMMON.TORSION' + include 'COMMON.INTERACT' + include 'COMMON.DERIV' + include 'COMMON.CHAIN' + include 'COMMON.NAMES' + include 'COMMON.IOUNITS' + include 'COMMON.FFIELD' + include 'COMMON.TORCNSTR' + include 'COMMON.CONTROL' + logical lprn + double precision thybt1(maxtermkcc) +C Set lprn=.true. for debugging + lprn=.false. +c lprn=.true. +C print *,"wchodze kcc" + if (lprn) write (iout,*) "ebend_kcc tor_mode",tor_mode + if (tor_mode.ne.2) etheta=0.0D0 + do i=ithet_start,ithet_end +c print *,i,itype(i-1),itype(i),itype(i-2) + if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1 + & .or.itype(i).eq.ntyp1) cycle + iti=itortyp_kcc(itype(i-1)) + sinthet=dsin(theta(i)/2.0d0) + costhet=dcos(theta(i)/2.0d0) + do j=1,nbend_kcc_Tb(iti) + thybt1(j)=v1bend_chyb(j,iti) + enddo + sumth1thyb=tschebyshev + & (1,nbend_kcc_Tb(iti),thybt1(1),costhet) + if (lprn) write (iout,*) i-1,itype(i-1),iti,theta(i)*rad2deg, + & sumth1thyb + ihelp=nbend_kcc_Tb(iti)-1 + gradthybt1=gradtschebyshev + & (0,ihelp,thybt1(1),costhet) + etheta=etheta+sumth1thyb +C print *,sumth1thyb,gradthybt1,sinthet*(-0.5d0) + gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang* + & gradthybt1*sinthet*(-0.5d0) + enddo + if (tor_mode.ne.2) then + ethetacnstr=0.0d0 +C print *,ithetaconstr_start,ithetaconstr_end,"TU" + do i=ithetaconstr_start,ithetaconstr_end + itheta=itheta_constr(i) + thetiii=theta(itheta) + difi=pinorm(thetiii-theta_constr0(i)) + if (difi.gt.theta_drange(i)) then + difi=difi-theta_drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else if (difi.lt.-drange(i)) then + difi=difi+drange(i) + ethetacnstr=ethetacnstr+0.25d0*for_thet_constr(i)*difi**4 + gloc(itheta+nphi-2,icg)=gloc(itheta+nphi-2,icg) + & +for_thet_constr(i)*difi**3 + else + difi=0.0 + endif + if (energy_dec) then + write (iout,'(a6,2i5,4f8.3,2e14.5)') "ethetc", + & i,itheta,rad2deg*thetiii, + & rad2deg*theta_constr0(i), rad2deg*theta_drange(i), + & rad2deg*difi,0.25d0*for_thet_constr(i)*difi**4, + & gloc(itheta+nphi-2,icg) + endif + enddo + endif + return + end c------------------------------------------------------------------------------ subroutine eback_sc_corr(esccor) c 7/21/2007 Correlations between the backbone-local and side-chain-local @@ -8745,9 +8874,9 @@ C--------------------------------------------------------------------------- & auxmat(2,2) iti1 = itortyp(itype(i+1)) if (j.lt.nres-1) then - itj1 = itortyp(itype(j+1)) + itj1 = itype2loc(itype(j+1)) else - itj1=ntortyp + itj1=nloctyp endif do iii=1,2 dipi(iii,1)=Ub2(iii,i) @@ -8835,16 +8964,16 @@ cd write (iout,*) "a_chujkl",((a_chuj(iii,jjj,kk,k),iii=1,2),jjj=1,2) if (l.eq.j+1) then C parallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itype2loc(itype(i)) else - iti=ntortyp + iti=nloctyp endif - itk1=itortyp(itype(k+1)) - itj=itortyp(itype(j)) + itk1=itype2loc(itype(k+1)) + itj=itype2loc(itype(j)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp + itl1=nloctyp endif C A1 kernel(j+1) A2T cd do iii=1,2 @@ -8988,17 +9117,17 @@ C End vectors else C Antiparallel orientation of the two CA-CA-CA frames. if (i.gt.1) then - iti=itortyp(itype(i)) + iti=itype2loc(itype(i)) else - iti=ntortyp + iti=nloctyp endif - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk1=itype2loc(itype(k+1)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp + itj1=nloctyp endif C A2 kernel(j-1)T A1T call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i), @@ -9336,9 +9465,9 @@ cd endif cd write (iout,*) cd & 'EELLO5: Contacts have occurred for peptide groups',i,j, cd & ' and',k,l - itk=itortyp(itype(k)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + itk=itype2loc(itype(k)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) eello5_1=0.0d0 eello5_2=0.0d0 eello5_3=0.0d0 @@ -9407,7 +9536,7 @@ C Cartesian gradient c goto 1112 c1111 continue C Contribution from graph II - call transpose2(EE(1,1,itk),auxmat(1,1)) + call transpose2(EE(1,1,k),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -9488,7 +9617,7 @@ C Cartesian gradient cd goto 1112 C Contribution from graph IV cd1110 continue - call transpose2(EE(1,1,itl),auxmat(1,1)) + call transpose2(EE(1,1,l),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -9561,7 +9690,7 @@ C Cartesian gradient cd goto 1112 C Contribution from graph IV 1110 continue - call transpose2(EE(1,1,itj),auxmat(1,1)) + call transpose2(EE(1,1,j),auxmat(1,1)) call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -9858,7 +9987,7 @@ C o o o o C C i i C C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - itk=itortyp(itype(k)) + itk=itype2loc(itype(k)) s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i)) s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k)) s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k)) @@ -10150,16 +10279,16 @@ C 4/7/01 AL Component s1 was removed, because it pertains to the respective C energy moment and not to the cluster cumulant. iti=itortyp(itype(i)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp + itj1=nloctyp endif - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) + itk=itype2loc(itype(k)) + itk1=itype2loc(itype(k+1)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp + itl1=nloctyp endif #ifdef MOMENT s1=dip(4,jj,i)*dip(4,kk,k) @@ -10168,7 +10297,7 @@ C energy moment and not to the cluster cumulant. s2=0.5d0*scalar2(b1(1,k),auxvec(1)) call matvec2(AECA(1,1,2),b1(1,l+1),auxvec(1)) s3=0.5d0*scalar2(b1(1,j+1),auxvec(1)) - call transpose2(EE(1,1,itk),auxmat(1,1)) + call transpose2(EE(1,1,k),auxmat(1,1)) call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1)) vv(1)=pizda(1,1)+pizda(2,2) vv(2)=pizda(2,1)-pizda(1,2) @@ -10266,24 +10395,24 @@ C C 4/7/01 AL Component s1 was removed, because it pertains to the respective C energy moment and not to the cluster cumulant. cd write (2,*) 'eello_graph4: wturn6',wturn6 - iti=itortyp(itype(i)) - itj=itortyp(itype(j)) + iti=itype2loc(itype(i)) + itj=itype2loc(itype(j)) if (j.lt.nres-1) then - itj1=itortyp(itype(j+1)) + itj1=itype2loc(itype(j+1)) else - itj1=ntortyp + itj1=nloctyp endif - itk=itortyp(itype(k)) + itk=itype2loc(itype(k)) if (k.lt.nres-1) then - itk1=itortyp(itype(k+1)) + itk1=itype2loc(itype(k+1)) else - itk1=ntortyp + itk1=nloctyp endif - itl=itortyp(itype(l)) + itl=itype2loc(itype(l)) if (l.lt.nres-1) then - itl1=itortyp(itype(l+1)) + itl1=itype2loc(itype(l+1)) else - itl1=ntortyp + itl1=nloctyp endif cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk, @@ -10503,11 +10632,11 @@ c j=i+4 k=i+1 l=i+3 - iti=itortyp(itype(i)) - itk=itortyp(itype(k)) - itk1=itortyp(itype(k+1)) - itl=itortyp(itype(l)) - itj=itortyp(itype(j)) + iti=itype2loc(itype(i)) + itk=itype2loc(itype(k)) + itk1=itype2loc(itype(k+1)) + itl=itype2loc(itype(l)) + itj=itype2loc(itype(j)) cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj cd write (2,*) 'i',i,' k',k,' j',j,' l',l cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then @@ -11284,6 +11413,7 @@ C now costhet_grad VofOverlap=VSolvSphere/2.0d0*(1.0-costhet)*(1.0-cosphi) & /VSolvSphere_div + & *wshield C now the gradient... C grad_shield is gradient of Calfa for peptide groups C write(iout,*) "shield_compon",i,k,VSolvSphere,scale_fac_dist, @@ -11345,20 +11475,193 @@ C-------------------------------------------------------------------------- implicit none include "DIMENSIONS" integer i,m,n - double precision x(n),y,yy(0:maxvar),aux -c Tschebyshev polynomial. Note that the first term is omitted + double precision x(n+1),y,yy(0:maxvar),aux +c Tschebyshev polynomial. Note that the first term is omitted c m=0: the constant term is included c m=1: the constant term is not included yy(0)=1.0d0 yy(1)=2.0d0*y do i=2,n - yy(i)=2*yy(1)*yy(i-1)-yy(i-2) + yy(i)=2*y*yy(i-1)-yy(i-2) enddo aux=0.0d0 do i=m,n - aux=aux+x(i)*yy(i) + aux=aux+x(i+1)*yy(i)*(i+1) +C print *, x(i+1),yy(i),i enddo gradtschebyshev=aux return end +C------------------------------------------------------------------------ +C first for shielding is setting of function of side-chains + subroutine set_shield_fac2 + implicit real*8 (a-h,o-z) + include 'DIMENSIONS' + include 'COMMON.CHAIN' + include 'COMMON.DERIV' + include 'COMMON.IOUNITS' + include 'COMMON.SHIELD' + include 'COMMON.INTERACT' +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 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 + ishield_list(i)=0 +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 + do k=1,nres + if ((itype(k).eq.ntyp1).or.(itype(k).eq.10)) cycle + dist_pep_side=0.0 + dist_side_calf=0.0 + do j=1,3 +C first lets set vector conecting the ithe side-chain with kth side-chain + pep_side(j)=c(j,k+nres)-(c(j,i)+c(j,i+1))/2.0d0 +C pep_side(j)=2.0d0 +C and vector conecting the side-chain with its proper calfa + side_calf(j)=c(j,k+nres)-c(j,k) +C side_calf(j)=2.0d0 + pept_group(j)=c(j,i)-c(j,i+1) +C lets have their lenght + dist_pep_side=pep_side(j)**2+dist_pep_side + dist_side_calf=dist_side_calf+side_calf(j)**2 + dist_pept_group=dist_pept_group+pept_group(j)**2 + enddo + dist_pep_side=dsqrt(dist_pep_side) + dist_pept_group=dsqrt(dist_pept_group) + dist_side_calf=dsqrt(dist_side_calf) + do j=1,3 + pep_side_norm(j)=pep_side(j)/dist_pep_side + side_calf_norm(j)=dist_side_calf + enddo +C now sscale fraction + sh_frac_dist=-(dist_pep_side-rpp(1,1)-buff_shield)/buff_shield +C print *,buff_shield,"buff" +C now sscale + if (sh_frac_dist.le.0.0) cycle +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 +C ishield_list is a list of non 0 side-chain that contribute to factor gradient +C this list is essential otherwise problem would be O3 + shield_list(ishield_list(i),i)=k +C Lets have the sscale value + if (sh_frac_dist.gt.1.0) then + scale_fac_dist=1.0d0 + do j=1,3 + sh_frac_dist_grad(j)=0.0d0 + enddo + else + scale_fac_dist=-sh_frac_dist*sh_frac_dist + & *(2.0d0*sh_frac_dist-3.0d0) + fac_help_scale=6.0d0*(sh_frac_dist-sh_frac_dist**2) + & /dist_pep_side/buff_shield*0.5d0 +C remember for the final gradient multiply sh_frac_dist_grad(j) +C for side_chain by factor -2 ! + do j=1,3 + sh_frac_dist_grad(j)=fac_help_scale*pep_side(j) +C sh_frac_dist_grad(j)=0.0d0 +C scale_fac_dist=1.0d0 +C print *,"jestem",scale_fac_dist,fac_help_scale, +C & sh_frac_dist_grad(j) + enddo + endif +C this is what is now we have the distance scaling now volume... + short=short_r_sidechain(itype(k)) + long=long_r_sidechain(itype(k)) + costhet=1.0d0/dsqrt(1.0d0+short**2/dist_pep_side**2) + sinthet=short/dist_pep_side*costhet +C now costhet_grad +C costhet=0.6d0 +C sinthet=0.8 + costhet_fac=costhet**3*short**2*(-0.5d0)/dist_pep_side**4 +C sinthet_fac=costhet**2*0.5d0*(short**3/dist_pep_side**4*costhet +C & -short/dist_pep_side**2/costhet) +C costhet_fac=0.0d0 + do j=1,3 + costhet_grad(j)=costhet_fac*pep_side(j) + enddo +C remember for the final gradient multiply costhet_grad(j) +C for side_chain by factor -2 ! +C fac alfa is angle between CB_k,CA_k, CA_i,CA_i+1 +C pep_side0pept_group is vector multiplication + pep_side0pept_group=0.0d0 + do j=1,3 + pep_side0pept_group=pep_side0pept_group+pep_side(j)*side_calf(j) + enddo + cosalfa=(pep_side0pept_group/ + & (dist_pep_side*dist_side_calf)) + fac_alfa_sin=1.0d0-cosalfa**2 + fac_alfa_sin=dsqrt(fac_alfa_sin) + rkprim=fac_alfa_sin*(long-short)+short +C rkprim=short + +C now costhet_grad + cosphi=1.0d0/dsqrt(1.0d0+rkprim**2/dist_pep_side**2) +C cosphi=0.6 + cosphi_fac=cosphi**3*rkprim**2*(-0.5d0)/dist_pep_side**4 + sinphi=rkprim/dist_pep_side/dsqrt(1.0d0+rkprim**2/ + & dist_pep_side**2) +C sinphi=0.8 + do j=1,3 + cosphi_grad_long(j)=cosphi_fac*pep_side(j) + &+cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa/ + &((dist_pep_side*dist_side_calf))* + &((side_calf(j))-cosalfa* + &((pep_side(j)/dist_pep_side)*dist_side_calf)) +C cosphi_grad_long(j)=0.0d0 + cosphi_grad_loc(j)=cosphi**3*0.5d0/dist_pep_side**2*(-rkprim) + &*(long-short)/fac_alfa_sin*cosalfa + &/((dist_pep_side*dist_side_calf))* + &(pep_side(j)- + &cosalfa*side_calf(j)/dist_side_calf*dist_pep_side) +C cosphi_grad_loc(j)=0.0d0 + enddo +C print *,sinphi,sinthet + VofOverlap=VSolvSphere/2.0d0*(1.0d0-dsqrt(1.0d0-sinphi*sinthet)) + & /VSolvSphere_div +C & *wshield +C now the gradient... + do j=1,3 + grad_shield(j,i)=grad_shield(j,i) +C gradient po skalowaniu + & +(sh_frac_dist_grad(j)*VofOverlap +C gradient po costhet + & +scale_fac_dist*VSolvSphere/VSolvSphere_div/4.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield +C grad_shield_side is Cbeta sidechain gradient + grad_shield_side(j,ishield_list(i),i)= + & (sh_frac_dist_grad(j)*-2.0d0 + & *VofOverlap + & -scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(-dsqrt(1.0d0-sinphi*sinthet))*( + & sinphi/sinthet*costhet*costhet_grad(j) + & +sinthet/sinphi*cosphi*cosphi_grad_long(j))) + & )*wshield + + grad_shield_loc(j,ishield_list(i),i)= + & scale_fac_dist*VSolvSphere/VSolvSphere_div/2.0d0* + &(1.0d0/(dsqrt(1.0d0-sinphi*sinthet))*( + & sinthet/sinphi*cosphi*cosphi_grad_loc(j) + & )) + & *wshield + enddo + 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) + enddo + return + end