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gbobc.f
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gbobc.f
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! This file is part of xtb4stda.
!
! Copyright (C) 2015-2019 Stefan Grimme
!
! xtb4stda is free software: you can redistribute it and/or modify it under
! the terms of the GNU Lesser General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! xtb4stda is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! GNU Lesser General Public License for more details.
!
! You should have received a copy of the GNU Lesser General Public License
! along with xtb4stda. If not, see <https://www.gnu.org/licenses/>.
module gbobc
implicit none
c cutoffs
c Born radii
real*8 :: lrcut_a=35.d0
c SASA = 2*(w+maxrasasa) + srcut_add
real*8 :: srcut_add=2.d0
c flag for gbsa
logical :: lgbsa
c number of particles
integer :: nat
c number of pairs
integer :: ntpair
c van der Waals radii of the particles
real*8, allocatable :: vdwr(:)
c greatest van der Waals radius
real*8 :: maxvdwr
c pair descreening approximation radii
real*8, allocatable :: rho(:)
c offset van der Waals radii
real*8, allocatable :: svdw(:)
c Neighbor list:
c cut-off radius for the Born radius NN list
real*8 :: lrcut
c cut-off radius for the SASA NN list
real*8 :: srcut
c number of neighbors for Born radii
integer :: nnrad
c number of neighbors for SASA computation
integer, allocatable :: nnsas(:)
c neighbors of an atom for Born radii
integer, allocatable :: nnlistr(:,:)
c neighbors of an atom for SASA
integer, allocatable :: nnlists(:,:)
c all pairs indeces array
integer, allocatable :: ppind(:,:)
c all pairs vector differences and magnitudes array
real*8, allocatable :: ddpair(:,:)
c angstroem to atomic unit
real*8, parameter :: atoau=1.d0/0.52917726d0
c atomic units to kcal
real*8, parameter :: autokcal=627.509541d0
c 4*pi
real*8, parameter :: pi4=12.56637061435916D0
c a.u. to eV
real*8, parameter :: autoeV=27.21138505d0
c GBOBC parameters
c offset parameter (fitted)
c real*8 :: soset=0.09d0*atoau
real*8 :: soset
c van der Waals to Lee-Richard's surface correction
real*8 :: alp=1.d0
real*8 :: bet=0.8d0
real*8 :: gam=4.85d0
c Smoothing dielectric function parameters
real*8, parameter :: w=0.3d0*atoau
real*8, parameter :: w3=w*(w*w)
real*8, parameter :: ah0=0.5d0
real*8, parameter :: ah1=3.d0/(4.d0*w)
real*8, parameter :: ah3=-1.d0/(4.d0*w3)
c Angular grid. 38 points lead rot.inv.errors for c60 of 2 kcal
integer, parameter :: nangsa=230
real*8 :: grida(4,nangsa)
include 'grida230.fh'
c integer, parameter :: nangsa=86
c include 'grida86.fh'
c integer, parameter :: nangsa=110
c include 'grida110.fh'
c real space cut-offs
real*8, parameter :: tolsesp=1.d-6
c Atom specific surface data
real*8, allocatable :: vdwsa(:)
real*8, allocatable :: wrp(:)
real*8, allocatable :: trj2(:,:)
c Dielectric data
real*8 :: gborn
real*8 :: epsv
real*8 :: epsu
real*8 :: keps
c Surface tension (mN/m=dyn/cm)
real*8, parameter :: mNmkcal=4.0305201015221386d-4
real*8 :: gammas
real*8 :: gamscale(94)
c Solvent density (g/cm^3) and molar mass (g/mol)
real*8, parameter :: molcm3au=8.92388d-2
real*8 :: smass
real*8 :: rhos
c Born radii
real*8 :: c1
real*8, allocatable :: brad(:)
real*8, allocatable :: brt(:)
c Salt screening
logical :: lsalt=.false.
real*8 :: ionst=0.d0
real*8 :: kappa_const=0.7897d-3
real*8 :: ion_rad=0.d0
real*8 :: kappa=0.d0
real*8, allocatable :: ionscr(:)
real*8, allocatable :: discr(:)
c Atomic surfaces
real*8 :: rprobe
real*8 :: sasamol
real*8 :: gsasa
real*8 :: sasagam
real*8, allocatable :: gamsasa(:)
real*8, allocatable :: sasa(:)
c Hydrogen bond contribution
logical :: lhb=.true.
real*8 :: ghb
real*8, allocatable :: hbw(:)
c Gradient:
c Born radii gradient
real*8, allocatable :: brdr(:,:,:)
c Molecular Surface gradient
real*8, allocatable :: dsdr(:,:)
real*8, allocatable :: dsdrp(:,:)
real*8, allocatable :: dsdrt(:,:,:)
c Hydrogen bond gradient
real*8, allocatable :: dhbdw(:)
c GB energy gradient
real*8, allocatable :: grdgb(:,:)
real*8, allocatable :: grddb(:)
real*8, allocatable :: dbrdp(:)
real*8, allocatable :: dgbta(:,:)
real*8, allocatable :: dgbtb(:)
c Parameters:
c van der Waals radii
real*8 :: rvdw(94)
c dielectric descreening parameters
real*8 :: sx(94)
c solvent accesible surface radii
real*8 :: rasasa(94)
c HB correction present if zero no HB correction
integer :: at_hb(94)
c solvent HB donor or acceptor strength
real*8 :: hb_mag(94)
c Gshift (gsolv=reference vs. gsolv)
real*8 :: gshift
integer, allocatable :: at(:)
save
contains
subroutine rd_rvdw(nat,at,sname,mode,temp)
implicit none
include 'setcommon.fh'
character*(*) sname
integer nat,at(nat),mode
integer :: i,fix,inum
real*8 :: rad
real*8 :: gamma_in, rvdwscal, tmp(94), gstate, dum, temp
character*80 fname
logical ex
character*200 a200
c D3 cut-off radii
rvdw(1:94)= (/
.1.09155,0.86735,1.7478 ,1.5491 ,1.608 ,1.45515,1.31125,1.24085,
.1.1498 ,1.0687 ,1.8541 ,1.74195,2.0053 ,1.89585,1.75085,1.65535,
.1.5523 ,1.4574 ,2.12055,2.05175,1.94515,1.8821 ,1.86055,1.7207,
.1.7731 ,1.72105,1.71635,1.6731 ,1.6504 ,1.61545,1.97895,1.93095,
.1.83125,1.7634 ,1.6831 ,1.6048 ,2.3088 ,2.2382 ,2.1098 ,2.02985,
.1.9298 ,1.87715,1.7845 ,1.73115,1.69875,1.67625,1.6654 ,1.731,
.2.13115,2.0937 ,2.0075 ,1.94505,1.869 ,1.79445,2.52835,2.5907,
.2.31305,2.31005,2.2851 ,2.26355,2.2448 ,2.22575,2.2117 ,2.06215,
.2.12135,2.07705,2.1397 ,2.1225 ,2.1104 ,2.0993 ,2.0065 ,2.1225,
.2.049 ,1.99275,1.94775,1.8745 ,1.7228 ,1.67625,1.6282 ,1.67995,
.2.15635,2.1382 ,2.05875,2.0027 ,1.9322 ,1.8608 ,2.5398 ,2.4647,
.2.35215,2.2126 ,2.2297 ,2.19785,2.17695,2.21705/)
c hydrogen bonding parameters
lhb=.false.
at_hb=0
at_hb(1)=1
at_hb(6)=1
at_hb(7)=1
at_hb(8)=1
at_hb(9)=1
at_hb(15)=1
at_hb(16)=1
at_hb(17)=1
at_hb(34)=1
at_hb(35)=1
at_hb(53)=1
rvdwscal=1.0d0
write(fname,'(''.param_gbsa_'',a)')trim(sname)
a200=trim(XTB4STDAHOME) // trim(fname)
fname=a200
write(*,*) 'Solvent : ', trim(sname)
write(*,*) 'GBSA parameter file : ', trim(fname)
inquire(file=fname,exist=ex)
if(.not.ex)then
write(*,*) 'solvent :',trim(sname),' not implemented'
stop 'init_gbsa'
endif
open(unit=1,file=fname)
read(1,*)epsv
read(1,*)smass
read(1,*)rhos
read(1,*)c1
read(1,*)rprobe
read(1,*)gshift
read(1,*)soset
read(1,*)dum
if(mode.eq.1) then ! gsolv=reference option in COSMOTHERM
c RT*(ln(ideal gas mol volume)+ln(rho/M))
gstate=(temp*8.31451/1000./4.184)*
. (log(24.79d0*temp/298.15)+
. log(1000.0d0*rhos/smass))
gshift=(gshift+gstate)/autokcal
write(*,*) 'Gsolv state corr. (kcal):',gstate
a200='gsolv=reference [X=1]'
elseif(mode.eq.0)then !gsolv option in COSMOTHERM to which it was fitted
gshift=gshift/autokcal
a200='gsolv [1 M gas/solution]'
elseif(mode.eq.2)then ! 1 bar gas/ 1 M solution is not implemented in COSMOTHERM although its the canonical choice
gstate=(temp*8.31451/1000./4.184)*log(24.79d0*temp/298.15)
gshift=(gshift+gstate)/autokcal
write(*,*) 'Gsolv state corr. (kcal):',gstate
a200='gsolv [1 bar gas/ 1 M solution]'
endif
do i=1,94
read(1,*)gamscale(i),sx(i),tmp(i)
if(abs(tmp(i)).gt.1.d-3) lhb=.true.
enddo
close(1)
c if(fit)then !penalty to avoid small sx which lead to numerical instabs
c dum=0
c do i=1,nat
c dum=dum+2.*(sx(at(i))-0.8)**4
c enddo
c gshift=gshift+dum/autokcal
c endif
c hydrogen bonding magnitude
hb_mag = -(tmp**2)/autokcal
c scaling of the van der Waals radius
rvdw = rvdw * rvdwscal
c add the probe radius to the molecular surface
rasasa=rvdw+rprobe
c surface tension scaling
gamma_in=1.0d0
gammas=gamma_in*(1.0d-5)*autokcal/mNmkcal
c dielectric scaling
epsu=1.d0
keps=((1.d0/epsv)-(1.d0/epsu))
c set the salt term
if(lsalt) then
c convert to au
ion_rad=ion_rad*atoau
c inverse Debye screening length
kappa=sqrt(epsv*temp*kappa_const/ionst)*atoau
kappa=1.d0/kappa
endif
c print parameters
write(*,*) 'Gsolv ref. state (COSMO-RS): ',trim(a200)
write(*,*) 'temperature (mdtemp) : ',temp
write(*,*) 'dielectric constant : ',epsv
write(*,*) 'rho : ',rhos
write(*,*) 'mass : ',smass
write(*,*) 'surface tension : ',gammas
write(*,*) 'probe radius : ',rprobe
write(*,*) 'vdW radii scaling : ',rvdwscal
write(*,*) 'Gshift (Eh) : ',gshift
write(*,*) 'c1 : ',c1
write(*,*) 'soset : ',soset
write(*,*) 'HB correction : ',lhb
if(lsalt) then
write(*,*) 'Debye screening length : ',1.d0/kappa/atoau
endif
soset=0.1*soset/0.52917726d0
rhos=rhos*molcm3au/smass
return
end subroutine rd_rvdw
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
subroutine init_gbsa(n12,at12,sname,mode,temp)
implicit none
character(20) :: sname
integer n12,mode
integer at12(n12)
real*8 temp
integer i,j,k
integer ierr
real*8 minvdwr
real*8 maxrasasa
real*8 r
call rd_rvdw(n12,at12,sname,mode,temp)
nat=n12
c initialize the vdw radii array
allocate(vdwr(nat))
allocate(rho(nat))
allocate(svdw(nat))
allocate(at(nat))
at=at12
maxvdwr=0.d0
minvdwr=1000.d0
do i=1,nat
vdwr(i)=rvdw(at12(i))*atoau
rho(i)=vdwr(i)*sx(at12(i))
svdw(i)=vdwr(i)-soset
maxvdwr=max(maxvdwr,vdwr(i))
minvdwr=min(minvdwr,vdwr(i))
enddo
c initialize Born radii
allocate(brad(nat),brt(nat))
allocate(brdr(3,nat,nat))
allocate(grdgb(3,nat),grddb(nat))
allocate(dbrdp(nat))
allocate(dgbta(3,nat),dgbtb(nat))
c nearest-neighbor list preparation
lrcut = lrcut_a*atoau
ntpair=nat*(nat-1)/2
allocate(nnlistr(3,ntpair),nnsas(nat),nnlists(nat,nat),
. ppind(2,ntpair),stat=ierr)
if(ierr.ne.0) stop 'Memory allocation failed!'
allocate(ddpair(4,ntpair),stat=ierr)
if(ierr.ne.0) stop 'Memory allocation failed!'
k=0
do i=1,nat
do j = 1,i-1
k=k+1
ppind(1,k)=i
ppind(2,k)=j
enddo
enddo
c initialize solvent-accessible atomic surface area computation (SASA)
allocate(vdwsa(nat))
allocate(wrp(nat))
allocate(trj2(2,nat))
allocate(sasa(nat),gamsasa(nat))
allocate(dsdr(3,nat),dsdrp(3,nat),dsdrt(3,nat,nat))
maxrasasa=0.d0
do i = 1, nat
vdwsa(i) = rasasa(at12(i))*atoau
maxrasasa=max(maxrasasa,vdwsa(i))
trj2(1,i) = (vdwsa(i)-w)**2
trj2(2,i) = (vdwsa(i)+w)**2
r=vdwsa(i)+w
wrp(i)=(0.25d0/w+
. 3.d0*ah3*(0.2d0*r*r-0.5*r*vdwsa(i)+
. vdwsa(i)*vdwsa(i)/3.))*r*r*r
r=vdwsa(i)-w
wrp(i)=wrp(i)-(0.25/w+
. 3.d0*ah3*(0.2d0*r*r-0.5*r*vdwsa(i)+
. vdwsa(i)*vdwsa(i)/3.))*r*r*r
enddo
srcut = 2.d0*(w + maxrasasa) + srcut_add*atoau
gammas=gammas*mNmkcal/autokcal
sasagam=pi4*gammas
do i = 1, nat
gamsasa(i)=gamscale(at12(i))*pi4*gammas
enddo
c initialize the hydrogen bonding contribution
ghb=0.d0
if(lhb) then
allocate(hbw(nat),dhbdw(nat))
endif
c initialize the salt term
if(lsalt) then
allocate(ionscr(nat),discr(nat))
endif
return
end subroutine init_gbsa
subroutine compute_fgb(n,xyz,fgb,fhb)
implicit none
integer n
real*8 xyz(3,n)
real*8 fgb(n,n)
real*8 fhb(n)
integer i,j,nnj
integer kk
real*8, parameter :: a13=1.d0/3.d0
real*8, parameter :: a4=0.25d0
real*8 aa,r2,gg,iepsu
real*8 dd,edd,dfgb,hkeps
c initialize
fgb=0.d0
hkeps=keps*autoeV
c compute Born radii
call compute_brad_sasa(n,xyz)
c compute the Debye-Hueckel ion exclusion term
if(lsalt) then
aa=0.5d0/epsv
do i = 1, n
gg=kappa*(brad(i)+ion_rad)
ionscr(i)=aa*exp(gg)/(1.d0+gg)
discr(i)=ionscr(i)*kappa*gg/(1.d0+gg)
enddo
endif
if(lsalt) then
iepsu=1.d0/epsu
c compute energy and fgb direct and radii derivatives
!$OMP PARALLEL PRIVATE(i,j,r2,aa,dd,edd,dfgb)
!$OMP DO
do kk = 1, ntpair
r2=ddpair(1,kk)
r2=r2*r2
i=ppind(1,kk)
j=ppind(2,kk)
aa=brad(i)*brad(j)
dd=a4*r2/aa
edd=exp(-dd)
dfgb=sqrt(r2+aa*edd)
gg=ionscr(i)+ionscr(j)
fgb(i,j)=autoeV*(exp(-kappa*dfgb)*gg-iepsu)/dfgb
fgb(j,i)=fgb(i,j)
enddo
!$OMP ENDDO
!$OMP END PARALLEL
c self-energy part
do i = 1, n
gg=ionscr(i)*2.d0
fgb(i,i)=autoeV*(exp(-kappa*brad(i))*gg-iepsu)/brad(i)
enddo
else
c compute energy and fgb direct and radii derivatives
!$OMP PARALLEL PRIVATE(i,j,r2,aa,dd,edd,dfgb)
!$OMP DO
do kk = 1, ntpair
r2=ddpair(1,kk)
r2=r2*r2
i=ppind(1,kk)
j=ppind(2,kk)
aa=brad(i)*brad(j)
dd=a4*r2/aa
edd=exp(-dd)
dfgb=1.d0/(r2+aa*edd)
fgb(i,j)=hkeps*sqrt(dfgb)
fgb(j,i)=fgb(i,j)
enddo
!$OMP ENDDO
!$OMP END PARALLEL
c self-energy part
do i = 1, n
fgb(i,i)=hkeps/brad(i)
enddo
endif
c compute the HB term
if(lhb) then
call compute_fhb(n,xyz,fhb)
else
fhb=0.d0
endif
return
end subroutine compute_fgb
subroutine compute_gb_egrad(n,xyz,q,gbornh,grd,lpr)
implicit none
integer n
real*8 xyz(3,n)
real*8 q(n)
real*8 gbornh
real*8 grd(3,n)
logical lpr
integer i,j,nnj
integer kk
real*8, parameter :: a13=1.d0/3.d0
real*8, parameter :: a4=0.25d0
real*8 aa,r2,fgb,br3
real*8 qq,dd,edd,dfgb,egb,ap,bp,qfg
real*8 gg,efg,epu
real*8 r0vdw,r01,r02,ar02
real*8 r(3)
real*8 kq(n)
c GB energy and gradient
if(.not.lsalt) then
c dielectric scaling of the charges
kq=keps*q
gborn=0.d0
grdgb=0.d0
grddb=0.d0
c compute energy and fgb direct and radii derivatives
!$OMP PARALLEL PRIVATE(i,j,r2,r,qq,aa,dd,edd,fgb,dfgb,egb,ap,bp),
!$OMP& PRIVATE(dgbta,dgbtb),REDUCTION(+:gborn,grdgb,grddb)
egb=0.d0
dgbta=0.d0
dgbtb=0.d0
!$OMP DO
do kk = 1, ntpair
r2=ddpair(1,kk)
r2=r2*r2
i=ppind(1,kk)
j=ppind(2,kk)
qq=q(i)*kq(j)
aa=brad(i)*brad(j)
dd=a4*r2/aa
edd=exp(-dd)
dfgb=1.d0/(r2+aa*edd)
fgb=qq*sqrt(dfgb)
dfgb=dfgb*fgb
egb=egb+fgb
ap=(1.d0-a4*edd)*dfgb
r(1)=ap*ddpair(2,kk)
r(2)=ap*ddpair(3,kk)
r(3)=ap*ddpair(4,kk)
dgbta(1,i)=dgbta(1,i)-r(1)
dgbta(2,i)=dgbta(2,i)-r(2)
dgbta(3,i)=dgbta(3,i)-r(3)
dgbta(1,j)=dgbta(1,j)+r(1)
dgbta(2,j)=dgbta(2,j)+r(2)
dgbta(3,j)=dgbta(3,j)+r(3)
bp=-0.5d0*edd*(1.d0+dd)*dfgb
dgbtb(i)=dgbtb(i)+brad(j)*bp
dgbtb(j)=dgbtb(j)+brad(i)*bp
enddo
!$OMP ENDDO
gborn=gborn+egb
grdgb=grdgb+dgbta
grddb=grddb+dgbtb
!$OMP END PARALLEL
c self-energy part
do i = 1, n
qq=q(i)/brad(i)
gborn=gborn+0.5d0*kq(i)*qq
grddb(i)=dbrdp(i)*(grddb(i)-0.5d0*keps*qq*qq)
enddo
c contract with the Born radii derivatives
!$OMP PARALLEL PRIVATE(dgbta,i,j), REDUCTION(+:grdgb)
dgbta=0.d0
!$OMP DO
do kk = 1, nnrad
i=nnlistr(1,kk)
j=nnlistr(2,kk)
dgbta(1,i)=dgbta(1,i)+grddb(j)*brdr(1,j,i)
dgbta(2,i)=dgbta(2,i)+grddb(j)*brdr(2,j,i)
dgbta(3,i)=dgbta(3,i)+grddb(j)*brdr(3,j,i)
dgbta(1,j)=dgbta(1,j)+grddb(i)*brdr(1,i,j)
dgbta(2,j)=dgbta(2,j)+grddb(i)*brdr(2,i,j)
dgbta(3,j)=dgbta(3,j)+grddb(i)*brdr(3,i,j)
enddo
!$OMP ENDDO
grdgb=grdgb+dgbta
!$OMP END PARALLEL
c self-energy part
do i = 1, n
grdgb(1,i)=grdgb(1,i)+grddb(i)*brdr(1,i,i)
grdgb(2,i)=grdgb(2,i)+grddb(i)*brdr(2,i,i)
grdgb(3,i)=grdgb(3,i)+grddb(i)*brdr(3,i,i)
enddo
else
c GB-SE energy and gradient
gborn=0.d0
grdgb=0.d0
grddb=0.d0
epu=1.d0/epsu
c compute energy and fgb direct and radii derivatives
!$OMP PARALLEL PRIVATE(i,j,r2,r,qq,aa,dd,edd,fgb,dfgb,egb,ap,bp,qfg),
!$OMP& PRIVATE(gg,efg,dgbta,dgbtb),REDUCTION(+:gborn,grdgb,grddb)
egb=0.d0
dgbta=0.d0
dgbtb=0.d0
!$OMP DO
do kk = 1, ntpair
r2=ddpair(1,kk)
r2=r2*r2
i=ppind(1,kk)
j=ppind(2,kk)
qq=q(i)*q(j)
aa=brad(i)*brad(j)
dd=a4*r2/aa
edd=exp(-dd)
dfgb=r2+aa*edd
fgb=sqrt(dfgb)
aa=kappa*fgb
efg=exp(-aa)
gg=(ionscr(i)+ionscr(j))*efg
qfg=qq/fgb
egb=egb+qfg*(gg-epu)
dfgb=qfg*(gg*(1.d0+aa)-epu)/dfgb
ap=(1.d0-a4*edd)*dfgb
r(1)=ap*ddpair(2,kk)
r(2)=ap*ddpair(3,kk)
r(3)=ap*ddpair(4,kk)
dgbta(1,i)=dgbta(1,i)-r(1)
dgbta(2,i)=dgbta(2,i)-r(2)
dgbta(3,i)=dgbta(3,i)-r(3)
dgbta(1,j)=dgbta(1,j)+r(1)
dgbta(2,j)=dgbta(2,j)+r(2)
dgbta(3,j)=dgbta(3,j)+r(3)
qfg=qfg*efg
bp=-0.5d0*edd*(1.d0+dd)*dfgb
dgbtb(i)=dgbtb(i)+brad(j)*bp+qfg*discr(i)
dgbtb(j)=dgbtb(j)+brad(i)*bp+qfg*discr(j)
enddo
!$OMP ENDDO
gborn=gborn+egb
grdgb=grdgb+dgbta
grddb=grddb+dgbtb
!$OMP END PARALLEL
c self-energy part
do i = 1, n
gg=exp(-kappa*brad(i))
aa=2.d0*ionscr(i)*gg-epu
qq=q(i)/brad(i)
gborn=gborn+0.5d0*qq*q(i)*aa
ap=aa-brad(i)*2.d0*(discr(i)+ionscr(i)*kappa)*gg
grddb(i)=dbrdp(i)*(grddb(i)-0.5d0*qq*qq*ap)
enddo
c contract with the Born radii derivatives
!$OMP PARALLEL PRIVATE(dgbta,i,j), REDUCTION(+:grdgb)
dgbta=0.d0
!$OMP DO
do kk = 1, nnrad
i=nnlistr(1,kk)
j=nnlistr(2,kk)
dgbta(1,i)=dgbta(1,i)+grddb(j)*brdr(1,j,i)
dgbta(2,i)=dgbta(2,i)+grddb(j)*brdr(2,j,i)
dgbta(3,i)=dgbta(3,i)+grddb(j)*brdr(3,j,i)
dgbta(1,j)=dgbta(1,j)+grddb(i)*brdr(1,i,j)
dgbta(2,j)=dgbta(2,j)+grddb(i)*brdr(2,i,j)
dgbta(3,j)=dgbta(3,j)+grddb(i)*brdr(3,i,j)
enddo
!$OMP ENDDO
grdgb=grdgb+dgbta
!$OMP END PARALLEL
c self-energy part
do i = 1, n
grdgb(1,i)=grdgb(1,i)+grddb(i)*brdr(1,i,i)
grdgb(2,i)=grdgb(2,i)+grddb(i)*brdr(2,i,i)
grdgb(3,i)=grdgb(3,i)+grddb(i)*brdr(3,i,i)
enddo
endif
gbornh = gborn
grd = grd + grdgb + dsdr
if(lhb) then
call compute_hb(n,q,grd)
endif
c if(lopt.and.lpr) then
c write(*,'(/,a)') 'Results GBOBC:'
c write(*,*) 'At #, Z , GBOBC (A), RVDW (A)'
c do i = 1, nat
c write(*,'(I5,2x,I2,6F12.4)') i,at(i),brad(i)/atoau,
c . rvdw(at(i)),sx(at(i)),xyz(1:3,i)/atoau
c enddo
c write(*,'(/,a)') 'Free Energy (kcal/mol):'
c write(*,'(''G-EL = '',F8.3)') gborn*autokcal
c write(*,'(''GCAV = '',F8.3)') gsasa*autokcal
c write(*,'(''G-HB = '',F8.3)') ghb*autokcal
c write(*,'(''GSOL = '',F8.3)') (gborn+gsasa+ghb)*autokcal
c endif
return
end subroutine compute_gb_egrad
subroutine compute_fhb(n,xyz,fhb)
implicit none
integer n
real*8 :: xyz(3,n)
real*8 :: fhb(n)
integer :: i
hbw=0.d0
dhbdw=0.d0
!$OMP PARALLEL DO
do i = 1, n
call compute_fhb_i(i,n,xyz)
enddo
!$OMP END PARALLELDO
fhb=hbw*autoeV
return
end subroutine compute_fhb
subroutine compute_fhb_i(i,n,xyz)
implicit none
integer :: i,n
real*8 :: xyz(3,n)
integer :: iz,nhb
real*8 :: hbed,dhbed
real*8 :: smaxd,sasad,sasaw
real*8 :: sfw,dsfw,w3,w2,w1
integer :: j
real*8 :: wbh,wah
c atomic Z
iz=at(i)
c number of HB
nhb=at_hb(iz)
if(nhb.gt.0) then
c SASA-D for HB
smaxd=1.d0/(vdwsa(i)*vdwsa(i)*gamsasa(i))
sasad=sasa(i)*smaxd
hbw(i)=hb_mag(iz)*sasad
dhbdw(i)=hb_mag(iz)*smaxd
endif
return
end subroutine compute_fhb_i
subroutine compute_hb(n,q,grd)
implicit none
integer :: n
real*8 :: q(n)
real*8 :: ghbh
real*8 :: grd(3,n)
integer :: i,j
real*8 :: dhbed
real*8 :: qq
ghb=0.d0
do i = 1, n
qq = q(i)*q(i)
ghb = ghb + hbw(i)*qq
enddo
!$OMP PARALLEL PRIVATE(dsdrp,j,dhbed), REDUCTION(+:grd)
dsdrp=0.d0
!$OMP DO
do i = 1, n
dhbed=dhbdw(i)
if(abs(dhbed).gt.0.d0) then
dhbed=dhbed*(q(i)*q(i))
do j = 1, n
dsdrp(1,j) = dsdrp(1,j) + dsdrt(1,j,i)*dhbed
dsdrp(2,j) = dsdrp(2,j) + dsdrt(2,j,i)*dhbed
dsdrp(3,j) = dsdrp(3,j) + dsdrt(3,j,i)*dhbed
enddo
endif
enddo
!$OMP ENDDO
grd=grd+dsdrp
!$OMP END PARALLEL
return
end subroutine compute_hb
subroutine compute_brad_sasa(n,xyz)
implicit none
integer n
real*8 :: xyz(3,n)
integer i,j,kk
real*8 brdrd(3,n)
real*8 brdrt(3,n)
brad=0.d0
dsdr=0.d0
dsdrt=0.d0
brdr=0.d0
brdrd=0.d0
c compute Born radii and their derivatives
!$OMP PARALLEL PRIVATE(brt,brdrt), REDUCTION(+:brad,brdrd)
brt=0.d0
brdrt=0.d0
!$OMP DO SCHEDULE(DYNAMIC,1)
do kk = 1, nnrad
call compute_psi(kk,brt,brdr,brdrt)
enddo
!$OMP ENDDO
brad=brad+brt
brdrd=brdrd+brdrt
!$OMP END PARALLEL
do i = 1, nat
brdr(1:3,i,i)=brdrd(1:3,i)
enddo
!$OMP PARALLELDO
do i = 1, nat
call compute_bornr(i,brad(i),dbrdp(i))
enddo
!$OMP END PARALLELDO
c compute solvent accessible surface and its derivatives
!$OMP PARALLEL DO SCHEDULE(DYNAMIC,1)
do i = 1, nat
call compute_numsa(n,xyz,i,vdwsa(i),sasa(i),dsdrt(:,:,i))
enddo
!$OMP END PARALLEL DO
!$OMP PARALLEL PRIVATE(dsdrp,j), REDUCTION(+:dsdr)
dsdrp=0.d0
!$OMP DO
do i = 1, nat
do j = 1, nat
dsdrp(1,j) = dsdrp(1,j) + dsdrt(1,j,i)
dsdrp(2,j) = dsdrp(2,j) + dsdrt(2,j,i)
dsdrp(3,j) = dsdrp(3,j) + dsdrt(3,j,i)
enddo
enddo
!$OMP ENDDO
dsdr=dsdr+dsdrp
!$OMP END PARALLEL
gsasa = sum(sasa)
return
end subroutine compute_brad_sasa
subroutine compute_bornr(iat,br,dpsi)
implicit none
integer iat
real*8 br
real*8 dpsi
real*8 svdwi,vdwri
real*8 s1,v1,s2
real*8 arg,arg2,th,ch
real*8 alpi,beti,gami
svdwi=svdw(iat)
vdwri=vdwr(iat)
s1=1.d0/svdwi
v1=1.d0/vdwri
s2=0.5d0*svdwi
br=br*s2
arg2=br*(gam*br-bet)
arg=br*(alp+arg2)
arg2=2.d0*arg2+alp+gam*br*br
th=tanh(arg)
ch=cosh(arg)
br=1.d0/(s1-v1*th)
c Include GBMV2-like scaling
br=c1*br
dpsi=ch*(s1-v1*th)
dpsi=s2*v1*arg2/(dpsi*dpsi)
dpsi=c1*dpsi
return
end subroutine compute_bornr
subroutine compute_psi(kk,br,gbr,gbrd)
implicit none
integer kk
real*8 br(nat),gbr(3,nat,nat),gbrd(3,nat)
integer ii,jj,nn
real*8 dr(3),r,rhoi,rhoj
real*8 gi,gj,ap,am,lnab,rhab,ab,dgi,dgj
real*8 drjj(3)
real*8 rh1,rhr1,r24,rh2,r1,aprh1,r12
real*8 rvdwi,rvdwj
integer ovij,ovji,ov
ii=nnlistr(1,kk)
jj=nnlistr(2,kk)
nn=nnlistr(3,kk)
r=ddpair(1,nn)
dr(1)=ddpair(2,nn)
dr(2)=ddpair(3,nn)
dr(3)=ddpair(4,nn)
rhoi=rho(ii)
rhoj=rho(jj)
rvdwi=vdwr(ii)
rvdwj=vdwr(jj)
ovij=1
ovji=1
if(r.ge.(rvdwi+rhoj)) ovij=0
if(r.ge.(rhoi+rvdwj)) ovji=0
ov=ovij+10*ovji
select case(ov)
c ij do not overlap; ji do not overlap
case(0)
c nonoverlaping spheres