!
use energy_data
use geometry_data, only:nres,deg2rad,c,dc,nres_molec
- use control_data, only:iscode
+ use control_data, only:iscode,dyn_ss
use io_base, only:rescode
- use control, only:setup_var,init_int_table
+ use control, only:setup_var,init_int_table,hpb_partition
use geometry, only:alloc_geo_arrays
use energy, only:alloc_ener_arrays
! implicit real*8 (a-h,o-z)
dhpb(i),ebr,forcon(i)
enddo
endif
+ if (ns.gt.0.and.dyn_ss) then
+ do i=nss+1,nhpb
+ ihpb(i-nss)=ihpb(i)
+ jhpb(i-nss)=jhpb(i)
+ forcon(i-nss)=forcon(i)
+ dhpb(i-nss)=dhpb(i)
+ enddo
+ nhpb=nhpb-nss
+ nss=0
+ call hpb_partition
+ do i=1,ns
+ dyn_ss_mask(iss(i))=.true.
+ enddo
+ endif
write (iout,'(a)')
return
end subroutine molread
real(kind=8) :: dwa16,akl,si,rri,epsij,rrij,sigeps,sigt1sq,epsijlip,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm, &
epspeptube,epssctube,sigmapeptube, &
- sigmasctube
+ sigmasctube,ssscale
real(kind=8) :: v0ij,v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,rjunk,&
res1
integer :: i,j,ichir1,ichir2,k,l,m,kk,ii,mm,junk,lll,ll,llll,n,jj
integer :: nlobi,iblock,maxinter,iscprol,ncatprotparm
character*3 string
-
+
!
! Body
!
vbl=3.8D0
vblinv=1.0D0/vbl
vblinv2=vblinv*vblinv
+ itime_mat=0
#ifndef CLUSTER
call card_concat(controlcard,.true.)
wname(4)="WCORRH"
!el
+ call reada(controlcard,"D0CM",d0cm,3.78d0)
+ call reada(controlcard,"AKCM",akcm,15.1d0)
+ call reada(controlcard,"AKTH",akth,11.0d0)
+ call reada(controlcard,"AKCT",akct,12.0d0)
+ call reada(controlcard,"V1SS",v1ss,-1.08d0)
+ call reada(controlcard,"V2SS",v2ss,7.61d0)
+ call reada(controlcard,"V3SS",v3ss,13.7d0)
+ call reada(controlcard,"EBR",ebr,-5.50D0)
+ call reada(controlcard,"ATRISS",atriss,0.301D0)
+ call reada(controlcard,"BTRISS",btriss,0.021D0)
+ call reada(controlcard,"CTRISS",ctriss,1.001D0)
+ call reada(controlcard,"DTRISS",dtriss,1.001D0)
+ call reada(controlcard,"SSSCALE",ssscale,1.0D0)
+ dyn_ss=(index(controlcard,'DYN_SS').gt.0)
+
allocate(ww(max_eneW))
do i=1,n_eneW
key = wname(i)(:ilen(wname(i)))
!
! Define the constants of the disulfide bridge
!
- ebr=-5.50D0
+! ebr=-5.50D0
!
! Old arbitrary potential - commented out.
!
! energy surface of diethyl disulfide.
! A. Liwo and U. Kozlowska, 11/24/03
!
- D0CM = 3.78d0
- AKCM = 15.1d0
- AKTH = 11.0d0
- AKCT = 12.0d0
- V1SS =-1.08d0
- V2SS = 7.61d0
- V3SS = 13.7d0
+! D0CM = 3.78d0
+! AKCM = 15.1d0
+! AKTH = 11.0d0
+! AKCT = 12.0d0
+! V1SS =-1.08d0
+! V2SS = 7.61d0
+! V3SS = 13.7d0
+#ifndef CLUSTER
+ if (dyn_ss) then
+ ss_depth=(ebr/wsc-0.25*eps(1,1))*ssscale
+ Ht=(Ht/wsc-0.25*eps(1,1))*ssscale
+ akcm=akcm/wsc*ssscale
+ akth=akth/wsc*ssscale
+ akct=akct/wsc*ssscale
+ v1ss=v1ss/wsc*ssscale
+ v2ss=v2ss/wsc*ssscale
+ v3ss=v3ss/wsc*ssscale
+ else
+ ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
+ endif
+#endif
if (lprint) then
write (iout,'(/a)') "Disulfide bridge parameters:"
write (iout,'(a,f10.2)') 'S-S bridge energy: ',ebr
subroutine read_general_data(*)
use control_data, only:indpdb,symetr,r_cut_ele,rlamb_ele,ions,&
- scelemode,TUBEmode,tor_mode
+ scelemode,TUBEmode,tor_mode,energy_dec
- use energy_data, only:distchainmax,tubeR0,tubecenter
+ use energy_data, only:distchainmax,tubeR0,tubecenter,dyn_ss
use geometry_data, only:boxxsize,boxysize,boxzsize,bordtubetop,&
bordtubebot,tubebufthick,buftubebot,buftubetop
! implicit none
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
call readi(controlcard,"SCELEMODE",scelemode,0)
call readi(controlcard,"OLDION",oldion,0)
-
+ dyn_ss=(index(controlcard,'DYN_SS').gt.0)
print *,"SCELE",scelemode
call readi(controlcard,'TORMODE',tor_mode,0)
!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
buftubetop=bordtubetop-tubebufthick
endif
ions=index(controlcard,"IONS").gt.0
- call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
+ call reada(controlcard,"R_CUT_ELE",r_cut_ele,25.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
write(iout,*) "R_CUT_ELE=",r_cut_ele
check_conf=index(controlcard,"NO_CHECK_CONF").eq.0