!
!-----------------------------------------------------------------------------
contains
-#if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
+#if !defined(WHAM_RUN) && !defined(CLUSTER)
!-----------------------------------------------------------------------------
! bank.F io_csa
!-----------------------------------------------------------------------------
use geometry_data
use energy_data
- use control_data, only:maxtor,maxterm
+ use control_data, only:maxterm !,maxtor
use MD_data
use MPI_data
!el use map_data
character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/)
logical :: lprint,LaTeX
real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob)
- real(kind=8),dimension(13) :: b
+ real(kind=8),dimension(13) :: bN
character(len=3) :: lancuch !,ucase
!el local variables
integer :: m,n,l,i,j,k,iblock,lll,llll,ll,nlobi,mm
real(kind=8) :: v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,si,&
dwa16,rjunk,akl,v0ij,rri,epsij,rrij,sigeps,sigt1sq,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm,&
- res1
+ res1,epsijlip,epspeptube,epssctube,sigmapeptube, &
+ sigmasctube
integer :: ichir1,ichir2
! real(kind=8),dimension(maxterm,-maxtor:maxtor,-maxtor:maxtor,2) :: v1_el,v2_el !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el allocate(v1_el(maxterm,-maxtor:maxtor,-maxtor:maxtor,2))
allocate(isc(ntyp+1)) !(ntyp+1)
allocate(restok(ntyp+1)) !(ntyp+1)
allocate(abond0(maxbondterm,ntyp)) !(maxbondterm,ntyp)
-
+ allocate(long_r_sidechain(ntyp))
+ allocate(short_r_sidechain(ntyp))
dsc(:)=0.0d0
dsc_inv(:)=0.0d0
endif
enddo
#else
- read (ibond,*) junk,vbldp0,akp,rjunk,mp,ip,pstok
+ read (ibond,*) junk,vbldp0,vbldpDUM,akp,rjunk,mp,ip,pstok
do i=1,ntyp
read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i),&
j=1,nbondterm(i)),msc(i),isc(i),restok(i)
allocate(bthet(2,-ntyp:ntyp,-1:1,-1:1)) !(2,-ntyp:ntyp,-1:1,-1:1)
allocate(polthet(0:3,-ntyp:ntyp)) !(0:3,-ntyp:ntyp)
allocate(gthet(3,-ntyp:ntyp)) !(3,-ntyp:ntyp)
- do i=-ntyp,ntyp
- a0thet(i)=0.0D0
- do j=1,2
- do ichir1=-1,1
- do ichir2=-1,1
- athet(j,i,ichir1,ichir2)=0.0D0
- bthet(j,i,ichir1,ichir2)=0.0D0
- enddo
- enddo
- enddo
- do j=0,3
- polthet(j,i)=0.0D0
- enddo
- do j=1,3
- gthet(j,i)=0.0D0
- enddo
- theta0(i)=0.0D0
- sig0(i)=0.0D0
- sigc0(i)=0.0D0
- enddo
+
+ a0thet(:)=0.0D0
+ athet(:,:,:,:)=0.0D0
+ bthet(:,:,:,:)=0.0D0
+ polthet(:,:)=0.0D0
+ gthet(:,:)=0.0D0
+ theta0(:)=0.0D0
+ sig0(:)=0.0D0
+ sigc0(:)=0.0D0
+ allocate(liptranene(ntyp))
+!C reading lipid parameters
+ write (iout,*) "iliptranpar",iliptranpar
+ call flush(iout)
+ read(iliptranpar,*) pepliptran
+ print *,pepliptran
+ do i=1,ntyp
+ read(iliptranpar,*) liptranene(i)
+ print *,liptranene(i)
+ enddo
+ close(iliptranpar)
#ifdef CRYST_THETA
!
!----------------------------------------------------
allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
- allocate(aa0thet(-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aa0thet(-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(aathet(ntheterm,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(aathet(ntheterm,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxtheterm,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(bbthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ccthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ddthet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(eethet(nsingle,ntheterm2,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(bbthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ccthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ddthet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(eethet(nsingle,ntheterm2,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
- allocate(ffthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
- allocate(ggthet(ndouble,ndouble,ntheterm3,-maxthetyp1:maxthetyp1,&
- -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
+ allocate(ffthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
+ allocate(ggthet(ndouble,ndouble,ntheterm3,-nthetyp-1:nthetyp+1,&
+ -nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,&
! -maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2))
do i=-ntyp1,-1
ithetyp(i)=-ithetyp(-i)
enddo
- do iblock=1,2
- do i=-maxthetyp,maxthetyp
- do j=-maxthetyp,maxthetyp
- do k=-maxthetyp,maxthetyp
- aa0thet(i,j,k,iblock)=0.0d0
- do l=1,ntheterm
- aathet(l,i,j,k,iblock)=0.0d0
- enddo
- do l=1,ntheterm2
- do m=1,nsingle
- bbthet(m,l,i,j,k,iblock)=0.0d0
- ccthet(m,l,i,j,k,iblock)=0.0d0
- ddthet(m,l,i,j,k,iblock)=0.0d0
- eethet(m,l,i,j,k,iblock)=0.0d0
- enddo
- enddo
- do l=1,ntheterm3
- do m=1,ndouble
- do mm=1,ndouble
- ffthet(mm,m,l,i,j,k,iblock)=0.0d0
- ggthet(mm,m,l,i,j,k,iblock)=0.0d0
- enddo
- enddo
- enddo
- enddo
- enddo
- enddo
- enddo
+
+ aa0thet(:,:,:,:)=0.0d0
+ aathet(:,:,:,:,:)=0.0d0
+ bbthet(:,:,:,:,:,:)=0.0d0
+ ccthet(:,:,:,:,:,:)=0.0d0
+ ddthet(:,:,:,:,:,:)=0.0d0
+ eethet(:,:,:,:,:,:)=0.0d0
+ ffthet(:,:,:,:,:,:,:)=0.0d0
+ ggthet(:,:,:,:,:,:,:)=0.0d0
+
! VAR:iblock means terminally blocking group 1=non-proline 2=proline
do iblock=1,2
! VAR:ntethtyp is type of theta potentials type currently 0=glycine
allocate(censc(3,maxlob,-ntyp:ntyp)) !(3,maxlob,-ntyp:ntyp)
allocate(gaussc(3,3,maxlob,-ntyp:ntyp)) !(3,3,maxlob,-ntyp:ntyp)
- do i=1,ntyp
- do j=1,maxlob
- bsc(j,i)=0.0D0
- nlob(i)=0
- enddo
- enddo
- nlob(ntyp1)=0
- dsc(ntyp1)=0.0D0
-
- do i=-ntyp,ntyp
- do j=1,maxlob
- do k=1,3
- censc(k,j,i)=0.0D0
- enddo
- do k=1,3
- do l=1,3
- gaussc(l,k,j,i)=0.0D0
- enddo
- enddo
- enddo
- enddo
-
+ bsc(:,:)=0.0D0
+ nlob(:)=0
+ nlob(:)=0
+ dsc(:)=0.0D0
+ censc(:,:,:)=0.0D0
+ gaussc(:,:,:,:)=0.0D0
+
#ifdef CRYST_SC
!
! Read the parameters of the probability distribution/energy expression
allocate(v1(maxterm,-ntortyp:ntortyp,-ntortyp:ntortyp,2))
allocate(v2(maxterm,-ntortyp:ntortyp,-ntortyp:ntortyp,2)) !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
!el---------------------------
- do iblock=1,2
- do i=-ntortyp,ntortyp
- do j=-ntortyp,ntortyp
- nterm(i,j,iblock)=0
- nlor(i,j,iblock)=0
- enddo
- enddo
- enddo
+ nterm(:,:,:)=0
+ nlor(:,:,:)=0
!el---------------------------
read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp)
do i=-ntyp,-1
itortyp(i)=-itortyp(-i)
enddo
-! itortyp(ntyp1)=ntortyp
-! itortyp(-ntyp1)=-ntortyp
+ itortyp(ntyp1)=ntortyp
+ itortyp(-ntyp1)=-ntortyp
do iblock=1,2
write (iout,*) 'ntortyp',ntortyp
do i=0,ntortyp-1
do i=0,nloctyp-1
read (ifourier,*,end=115,err=115)
- read (ifourier,*,end=115,err=115) (b(ii),ii=1,13)
+ read (ifourier,*,end=115,err=115) (bN(ii),ii=1,13)
if (lprint) then
write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii),ii=1,13)
+ write (iout,'(a,i2,a,f10.5)') ('bN(',ii,')=',bN(ii),ii=1,13)
endif
- B1(1,i) = b(3)
- B1(2,i) = b(5)
- B1(1,-i) = b(3)
- B1(2,-i) = -b(5)
+ B1(1,i) = bN(3)
+ B1(2,i) = bN(5)
+ B1(1,-i) = bN(3)
+ B1(2,-i) = -bN(5)
! b1(1,i)=0.0d0
! b1(2,i)=0.0d0
- B1tilde(1,i) = b(3)
- B1tilde(2,i) =-b(5)
- B1tilde(1,-i) =-b(3)
- B1tilde(2,-i) =b(5)
+ B1tilde(1,i) = bN(3)
+ B1tilde(2,i) =-bN(5)
+ B1tilde(1,-i) =-bN(3)
+ B1tilde(2,-i) =bN(5)
! b1tilde(1,i)=0.0d0
! b1tilde(2,i)=0.0d0
- B2(1,i) = b(2)
- B2(2,i) = b(4)
- B2(1,-i) =b(2)
- B2(2,-i) =-b(4)
+ B2(1,i) = bN(2)
+ B2(2,i) = bN(4)
+ B2(1,-i) =bN(2)
+ B2(2,-i) =-bN(4)
! b2(1,i)=0.0d0
! b2(2,i)=0.0d0
- CC(1,1,i)= b(7)
- CC(2,2,i)=-b(7)
- CC(2,1,i)= b(9)
- CC(1,2,i)= b(9)
- CC(1,1,-i)= b(7)
- CC(2,2,-i)=-b(7)
- CC(2,1,-i)=-b(9)
- CC(1,2,-i)=-b(9)
+ CC(1,1,i)= bN(7)
+ CC(2,2,i)=-bN(7)
+ CC(2,1,i)= bN(9)
+ CC(1,2,i)= bN(9)
+ CC(1,1,-i)= bN(7)
+ CC(2,2,-i)=-bN(7)
+ CC(2,1,-i)=-bN(9)
+ CC(1,2,-i)=-bN(9)
! CC(1,1,i)=0.0d0
! CC(2,2,i)=0.0d0
! CC(2,1,i)=0.0d0
! CC(1,2,i)=0.0d0
- Ctilde(1,1,i)=b(7)
- Ctilde(1,2,i)=b(9)
- Ctilde(2,1,i)=-b(9)
- Ctilde(2,2,i)=b(7)
- Ctilde(1,1,-i)=b(7)
- Ctilde(1,2,-i)=-b(9)
- Ctilde(2,1,-i)=b(9)
- Ctilde(2,2,-i)=b(7)
+ Ctilde(1,1,i)=bN(7)
+ Ctilde(1,2,i)=bN(9)
+ Ctilde(2,1,i)=-bN(9)
+ Ctilde(2,2,i)=bN(7)
+ Ctilde(1,1,-i)=bN(7)
+ Ctilde(1,2,-i)=-bN(9)
+ Ctilde(2,1,-i)=bN(9)
+ Ctilde(2,2,-i)=bN(7)
! Ctilde(1,1,i)=0.0d0
! Ctilde(1,2,i)=0.0d0
! Ctilde(2,1,i)=0.0d0
! Ctilde(2,2,i)=0.0d0
- DD(1,1,i)= b(6)
- DD(2,2,i)=-b(6)
- DD(2,1,i)= b(8)
- DD(1,2,i)= b(8)
- DD(1,1,-i)= b(6)
- DD(2,2,-i)=-b(6)
- DD(2,1,-i)=-b(8)
- DD(1,2,-i)=-b(8)
+ DD(1,1,i)= bN(6)
+ DD(2,2,i)=-bN(6)
+ DD(2,1,i)= bN(8)
+ DD(1,2,i)= bN(8)
+ DD(1,1,-i)= bN(6)
+ DD(2,2,-i)=-bN(6)
+ DD(2,1,-i)=-bN(8)
+ DD(1,2,-i)=-bN(8)
! DD(1,1,i)=0.0d0
! DD(2,2,i)=0.0d0
! DD(2,1,i)=0.0d0
! DD(1,2,i)=0.0d0
- Dtilde(1,1,i)=b(6)
- Dtilde(1,2,i)=b(8)
- Dtilde(2,1,i)=-b(8)
- Dtilde(2,2,i)=b(6)
- Dtilde(1,1,-i)=b(6)
- Dtilde(1,2,-i)=-b(8)
- Dtilde(2,1,-i)=b(8)
- Dtilde(2,2,-i)=b(6)
+ Dtilde(1,1,i)=bN(6)
+ Dtilde(1,2,i)=bN(8)
+ Dtilde(2,1,i)=-bN(8)
+ Dtilde(2,2,i)=bN(6)
+ Dtilde(1,1,-i)=bN(6)
+ Dtilde(1,2,-i)=-bN(8)
+ Dtilde(2,1,-i)=bN(8)
+ Dtilde(2,2,-i)=bN(6)
! Dtilde(1,1,i)=0.0d0
! Dtilde(1,2,i)=0.0d0
! Dtilde(2,1,i)=0.0d0
! Dtilde(2,2,i)=0.0d0
- EE(1,1,i)= b(10)+b(11)
- EE(2,2,i)=-b(10)+b(11)
- EE(2,1,i)= b(12)-b(13)
- EE(1,2,i)= b(12)+b(13)
- EE(1,1,-i)= b(10)+b(11)
- EE(2,2,-i)=-b(10)+b(11)
- EE(2,1,-i)=-b(12)+b(13)
- EE(1,2,-i)=-b(12)-b(13)
+ EE(1,1,i)= bN(10)+bN(11)
+ EE(2,2,i)=-bN(10)+bN(11)
+ EE(2,1,i)= bN(12)-bN(13)
+ EE(1,2,i)= bN(12)+bN(13)
+ EE(1,1,-i)= bN(10)+bN(11)
+ EE(2,2,-i)=-bN(10)+bN(11)
+ EE(2,1,-i)=-bN(12)+bN(13)
+ EE(1,2,-i)=-bN(12)-bN(13)
! ee(1,1,i)=1.0d0
! ee(2,2,i)=1.0d0
allocate(eps_scp(ntyp,2),rscp(ntyp,2)) !(ntyp,2)
allocate(sigma0(ntyp),rr0(ntyp),sigii(ntyp)) !(ntyp)
allocate(chip(ntyp1),alp(ntyp1)) !(ntyp)
- do i=1,ntyp
- do j=1,ntyp
- augm(i,j)=0.0D0
- enddo
- chip(i)=0.0D0
- alp(i)=0.0D0
- sigma0(i)=0.0D0
- sigii(i)=0.0D0
- rr0(i)=0.0D0
- enddo
+ allocate(epslip(ntyp,ntyp))
+ augm(:,:)=0.0D0
+ chip(:)=0.0D0
+ alp(:)=0.0D0
+ sigma0(:)=0.0D0
+ sigii(:)=0.0D0
+ rr0(:)=0.0D0
+
!--------------------------------
read (isidep,*,end=117,err=117) ipot,expon
read (isidep,*,end=117,err=117)(sigii(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(chip(i),i=1,ntyp)
read (isidep,*,end=117,err=117)(alp(i),i=1,ntyp)
+ do i=1,ntyp
+ read (isidep,*,end=117,err=117)(epslip(i,j),j=i,ntyp)
+ enddo
+
! For the GB potential convert sigma'**2 into chi'
if (ipot.eq.4) then
do i=1,ntyp
! Calculate the "working" parameters of SC interactions.
!el from module energy - COMMON.INTERACT-------
- allocate(aa(ntyp1,ntyp1),bb(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
allocate(sigma(0:ntyp1,0:ntyp1),r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
- do i=1,ntyp1
- do j=1,ntyp1
- aa(i,j)=0.0D0
- bb(i,j)=0.0D0
- chi(i,j)=0.0D0
- sigma(i,j)=0.0D0
- r0(i,j)=0.0D0
- enddo
- enddo
+ allocate(acavtub(ntyp1),bcavtub(ntyp1),ccavtub(ntyp1),&
+ dcavtub(ntyp1))
+ allocate(sc_aa_tube_par(ntyp1),sc_bb_tube_par(ntyp1),&
+ tubetranene(ntyp1))
+ aa_aq(:,:)=0.0D0
+ bb_aq(:,:)=0.0D0
+ aa_lip(:,:)=0.0D0
+ bb_lip(:,:)=0.0D0
+ chi(:,:)=0.0D0
+ sigma(:,:)=0.0D0
+ r0(:,:)=0.0D0
+ acavtub(:)=0.0d0
+ bcavtub(:)=0.0d0
+ ccavtub(:)=0.0d0
+ dcavtub(:)=0.0d0
+ sc_aa_tube_par(:)=0.0d0
+ sc_bb_tube_par(:)=0.0d0
+
!--------------------------------
do i=2,ntyp
do j=1,i-1
eps(i,j)=eps(j,i)
+ epslip(i,j)=epslip(j,i)
enddo
enddo
do i=1,ntyp
epsij=eps(i,j)
sigeps=dsign(1.0D0,epsij)
epsij=dabs(epsij)
- aa(i,j)=epsij*rrij*rrij
- bb(i,j)=-sigeps*epsij*rrij
- aa(j,i)=aa(i,j)
- bb(j,i)=bb(i,j)
+ aa_aq(i,j)=epsij*rrij*rrij
+ bb_aq(i,j)=-sigeps*epsij*rrij
+ aa_aq(j,i)=aa_aq(i,j)
+ bb_aq(j,i)=bb_aq(i,j)
+ epsijlip=epslip(i,j)
+ sigeps=dsign(1.0D0,epsijlip)
+ epsijlip=dabs(epsijlip)
+ aa_lip(i,j)=epsijlip*rrij*rrij
+ bb_lip(i,j)=-sigeps*epsijlip*rrij
+ aa_lip(j,i)=aa_lip(i,j)
+ bb_lip(j,i)=bb_lip(i,j)
+!C write(iout,*) aa_lip
if (ipot.gt.2) then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
endif
if (lprint) then
write (iout,'(2(a3,2x),3(1pe10.3),5(0pf8.3))') &
- restyp(i),restyp(j),aa(i,j),bb(i,j),augm(i,j),&
+ restyp(i),restyp(j),aa_aq(i,j),bb_aq(i,j),augm(i,j),&
sigma(i,j),r0(i,j),chi(i,j),chi(j,i)
endif
enddo
enddo
-
- allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
+ write(iout,*) "tube param"
+ read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep, &
+ ccavtubpep,dcavtubpep,tubetranenepep
+ sigmapeptube=sigmapeptube**6
+ sigeps=dsign(1.0D0,epspeptube)
+ epspeptube=dabs(epspeptube)
+ pep_aa_tube=4.0d0*epspeptube*sigmapeptube**2
+ pep_bb_tube=-sigeps*4.0d0*epspeptube*sigmapeptube
+ write(iout,*) pep_aa_tube,pep_bb_tube,tubetranenepep
do i=1,ntyp
- do j=1,2
- bad(i,j)=0.0D0
- enddo
+ read(itube,*) epssctube,sigmasctube,acavtub(i),bcavtub(i), &
+ ccavtub(i),dcavtub(i),tubetranene(i)
+ sigmasctube=sigmasctube**6
+ sigeps=dsign(1.0D0,epssctube)
+ epssctube=dabs(epssctube)
+ sc_aa_tube_par(i)=4.0d0*epssctube*sigmasctube**2
+ sc_bb_tube_par(i)=-sigeps*4.0d0*epssctube*sigmasctube
+ write(iout,*) sc_aa_tube_par(i), sc_bb_tube_par(i),tubetranene(i)
enddo
+ allocate(aad(ntyp,2),bad(ntyp,2)) !(ntyp,2)
+ bad(:,:)=0.0D0
+
#ifdef OLDSCP
!
! Define the SC-p interaction constants (hard-coded; old style)
goto 10
else if (card(:3).eq.'TER') then
! End current chain
- ires_old=ires+1
+ ires_old=ires+2
ishift1=ishift1+1
itype(ires_old)=ntyp1
+ itype(ires_old-1)=ntyp1
ibeg=2
! write (iout,*) "Chain ended",ires,ishift,ires_old
if (unres_pdb) then
enddo
else
call sccenter(ires,iii,sccor)
+! iii=0
endif
iii=0
endif
! write (iout,*) "Calculating sidechain center iii",iii
if (unres_pdb) then
do j=1,3
- dc(j,ires+nres)=sccor(j,iii)
+ dc(j,ires+ishift1-ishift-1)=sccor(j,iii)
enddo
else
call sccenter(ires_old,iii,sccor)
nres=ires
do i=2,nres-1
! write (iout,*) i,itype(i)
- if (itype(i).eq.ntyp1) then
+! if (itype(i).eq.ntyp1) then
! write (iout,*) "dummy",i,itype(i)
- do j=1,3
- c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
+! do j=1,3
+! c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2
! c(j,i)=(c(j,i-1)+c(j,i+1))/2
- dc(j,i)=c(j,i)
- enddo
- endif
+! dc(j,i)=c(j,i)
+! enddo
+! endif
+ if (itype(i).eq.ntyp1) then
+ if (itype(i+1).eq.ntyp1) then
+! 16/01/2014 by Adasko: Adding to dummy atoms in the chain
+! first is connected prevous chain (itype(i+1).eq.ntyp1)=true
+! second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the last dummy residue
+! print *,i,'tu dochodze'
+ call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif !fail
+ print *,i,'a tu?'
+ do j=1,3
+ c(j,i)=c(j,i-1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i-2)-c(j,i-3))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i-1)+dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ else !itype(i+1).eq.ntyp1
+ if (unres_pdb) then
+! 2/15/2013 by Adam: corrected insertion of the first dummy residue
+ call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
+ if (fail) then
+ e2(1)=0.0d0
+ e2(2)=1.0d0
+ e2(3)=0.0d0
+ endif
+ do j=1,3
+ c(j,i)=c(j,i+1)-1.9d0*e2(j)
+ enddo
+ else !unres_pdb
+ do j=1,3
+ dcj=(c(j,i+3)-c(j,i+2))/2.0
+ if (dcj.eq.0) dcj=1.23591524223
+ c(j,i)=c(j,i+1)-dcj
+ c(j,nres+i)=c(j,i)
+ enddo
+ endif !unres_pdb
+ endif !itype(i+1).eq.ntyp1
+ endif !itype.eq.ntyp1
+
enddo
! Calculate the CM of the last side chain.
if (iii.gt.0) then
e2(3)=0.0d0
endif
do j=1,3
- c(j,nres)=c(j,nres-1)-3.8d0*e2(j)
+ c(j,nres)=c(j,nres-1)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,nres-2)-c(j,nres-3)
+ dcj=(c(j,nres-2)-c(j,nres-3))/2.0
c(j,nres)=c(j,nres-1)+dcj
c(j,2*nres)=c(j,nres)
enddo
endif
endif
+!el kontrola nres w pliku inputowym WHAM-a w porownaniu z wartoscia wczytana z pliku pdb
+#ifdef WHAM_RUN
+ if (nres.ne.nres0) then
+ write (iout,*) "Error: wrong parameter value: NRES=",nres,&
+ " NRES0=",nres0
+ stop "Error nres value in WHAM input"
+ endif
+#endif
!---------------------------------
!el reallocate tables
! do i=1,maxres/3
e2(3)=0.0d0
endif
do j=1,3
- c(j,1)=c(j,2)-3.8d0*e2(j)
+ c(j,1)=c(j,2)-1.9d0*e2(j)
enddo
else
do j=1,3
- dcj=c(j,4)-c(j,3)
+ dcj=(c(j,4)-c(j,3))/2.0
c(j,1)=c(j,2)-dcj
c(j,nres+1)=c(j,1)
enddo
(c(j,ires+nres),j=1,3)
enddo
endif
+! znamy już nres wiec mozna alokowac tablice
! Calculate internal coordinates.
if(me.eq.king.or..not.out1file)then
write (iout,'(a)') &
!!!el
if(.not.allocated(theta)) then
allocate(theta(nres+2))
-! allocate(phi(nres+2))
-! allocate(alph(nres+2))
-! allocate(omeg(nres+2))
- do i=1,nres+2
- theta(i)=0.0d0
-! phi(i)=0.0d0
-! alph(i)=0.0d0
-! omeg(i)=0.0d0
- enddo
+ theta(:)=0.0d0
endif
-! allocate(costtab(nres))
-! allocate(sinttab(nres))
-! allocate(cost2tab(nres))
-! allocate(sint2tab(nres))
-! allocate(xxref(nres))
-! allocate(yyref(nres))
-! allocate(zzref(nres)) !(maxres)
-! do i=1,nres
-! costtab(i)=0.0d0
-! sinttab(i)=0.0d0
-! cost2tab(i)=0.0d0
-! sint2tab(i)=0.0d0
-! xxref(i)=0.0d0
-! yyref(i)=0.0d0
-! zzref(i)=0.0d0
-! enddo
-
-! endif
+
if(.not.allocated(phi)) allocate(phi(nres+2))
if(.not.allocated(alph)) allocate(alph(nres+2))
if(.not.allocated(omeg)) allocate(omeg(nres+2))
if(.not.allocated(dc_norm)) then
! if(.not.allocated(dc_norm)) allocate(dc_norm(3,0:2*nres+2))
allocate(dc_norm(3,0:2*nres+2))
- do i=0,2*nres+2
- dc_norm(1,i)=0.d0
- dc_norm(2,i)=0.d0
- dc_norm(3,i)=0.d0
- enddo
+ dc_norm(:,:)=0.d0
endif
call int_from_cart(.true.,.false.)
- call sc_loc_geom(.true.)
-! call sc_loc_geom(.false.)
-! wczesbiej bylo false
+ call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
! enddiagnostic
! makes copy of chains
write (iout,*) "symetr", symetr
+ do j=1,3
+ dc(j,0)=c(j,1)
+ enddo
if (symetr.gt.1) then
call permut(symetr)
return
end subroutine readpdb
-#if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
+#if !defined(WHAM_RUN) && !defined(CLUSTER)
!-----------------------------------------------------------------------------
! readrtns_CSA.F
!-----------------------------------------------------------------------------
character(len=640) :: controlcard
real(kind=8) :: seed,rmsdbc,rmsdbc1max,rmsdbcm,drms,timem!,&
-
+ integer i
nglob_csa=0
eglob_csa=1d99
timem=timlim
modecalc=0
call reada(controlcard,"T_BATH",t_bath,300.0d0)
+!C SHIELD keyword sets if the shielding effect of side-chains is used
+!C 0 denots no shielding is used all peptide are equally despite the
+!C solvent accesible area
+!C 1 the newly introduced function
+!C 2 reseved for further possible developement
+ call readi(controlcard,'SHIELD',shield_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "shield_mode",shield_mode
+!C Varibles set size of box
+ with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
+ write (iout,*) "with_theta_constr ",with_theta_constr
+ AFMlog=(index(controlcard,'AFM'))
+ selfguide=(index(controlcard,'SELFGUIDE'))
+ print *,'AFMlog',AFMlog,selfguide,"KUPA"
+ call readi(controlcard,'GENCONSTR',genconstr,0)
+ call reada(controlcard,'BOXX',boxxsize,100.0d0)
+ call reada(controlcard,'BOXY',boxysize,100.0d0)
+ call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ call readi(controlcard,'TUBEMOD',tubemode,0)
+ write (iout,*) TUBEmode,"TUBEMODE"
+ if (TUBEmode.gt.0) then
+ call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+ call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+ call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
+ call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+ call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+ call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+ call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+ buftubebot=bordtubebot+tubebufthick
+ buftubetop=bordtubetop-tubebufthick
+ endif
+
+! CUTOFFF ON ELECTROSTATICS
+ call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
+ write(iout,*) "R_CUT_ELE=",r_cut_ele
+! Lipidic parameters
+ call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
+ call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
+ if (lipthick.gt.0.0d0) then
+ bordliptop=(boxzsize+lipthick)/2.0
+ bordlipbot=bordliptop-lipthick
+ if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0)) &
+ write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
+ buflipbot=bordlipbot+lipbufthick
+ bufliptop=bordliptop-lipbufthick
+ if ((lipbufthick*2.0d0).gt.lipthick) &
+ write(iout,*) "WARNING WRONG SIZE OF LIP AQ BUF"
+ endif !lipthick.gt.0
+ write(iout,*) "bordliptop=",bordliptop
+ write(iout,*) "bordlipbot=",bordlipbot
+ write(iout,*) "bufliptop=",bufliptop
+ write(iout,*) "buflipbot=",buflipbot
+ write (iout,*) "SHIELD MODE",shield_mode
+
+!C-------------------------
minim=(index(controlcard,'MINIMIZE').gt.0)
dccart=(index(controlcard,'CART').gt.0)
overlapsc=(index(controlcard,'OVERLAP').gt.0)
if(me.eq.king.or..not.out1file) &
write (iout,'(2a)') diagmeth(kdiag),&
' routine used to diagonalize matrices.'
+ if (shield_mode.gt.0) then
+ pi=3.141592d0
+!C VSolvSphere the volume of solving sphere
+!C print *,pi,"pi"
+!C rpp(1,1) is the energy r0 for peptide group contact and will be used for it
+!C there will be no distinction between proline peptide group and normal peptide
+!C group in case of shielding parameters
+ VSolvSphere=4.0/3.0*pi*rpp(1,1)**3
+ VSolvSphere_div=VSolvSphere-4.0/3.0*pi*(rpp(1,1)/2.0)**3
+ write (iout,*) VSolvSphere,VSolvSphere_div
+!C long axis of side chain
+ do i=1,ntyp
+ long_r_sidechain(i)=vbldsc0(1,i)
+ short_r_sidechain(i)=sigma0(i)
+ write(iout,*) "parame for long and short axis",i,vbldsc0(1,i),&
+ sigma0(i)
+ enddo
+ buff_shield=1.0d0
+ endif
return
end subroutine read_control
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
subroutine openunits
- use energy_data, only: usampl
+ use MD_data, only: usampl
use csa_data
use MPI_data
use control_data, only:out1file
! print *,"Processor",myrank," opened file IELEP"
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',action='read')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+
! print *,"Processor",myrank," opened file ISIDEP"
! print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
open (ielep,file=elename,status='old')
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old')
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',&
readonly)
open (ielep,file=elename,status='old',readonly)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',action='read')
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',action='read')
+
#ifndef CRYST_SC
call getenv_loc('ROTPARPDB',rotname_pdb)
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
subroutine readrst
use geometry_data, only: nres,dc
- use energy_data, only: usampl,iset
use MD_data
! implicit real*8 (a-h,o-z)
! include 'DIMENSIONS'
open(irest2,file=rest2name,status='unknown')
read(irest2,*) totT,EK,potE,totE,t_bath
- do i=1,2*nres
+ totTafm=totT
+! do i=1,2*nres
+! AL 4/17/17: Now reading d_t(0,:) too
+ do i=0,2*nres
read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
enddo
- do i=1,2*nres
+! do i=1,2*nres
+! AL 4/17/17: Now reading d_c(0,:) too
+ do i=0,2*nres
read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
enddo
if(usampl) then
projects / unres4.git / blobdiff