with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
write (iout,*) "with_theta_constr ",with_theta_constr
call readi(controlcard,'SYM',symetr,1)
- call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
+ call reada(controlcard,'TIMLIM',timlim,2800.0D0) ! default 16 hours
unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
AFMlog=(index(controlcard,'AFM'))
selfguide=(index(controlcard,'SELFGUIDE'))
print *,'AFMlog',AFMlog,selfguide,"KUPA"
+ call readi(controlcard,'TUBEMOD',tubelog,0)
+ write (iout,*) TUBElog,"TUBEMODE"
+ call readi(controlcard,'GENCONSTR',genconstr,0)
+C write (iout,*) TUBElog,"TUBEMODE"
call readi(controlcard,'IPRINT',iprint,0)
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 if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
write(iout,*) "shield_mode",shield_mode
C endif
+ call readi(controlcard,'TORMODE',tor_mode,0)
+C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "torsional and valence angle mode",tor_mode
call readi(controlcard,'MAXGEN',maxgen,10000)
call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
call readi(controlcard,"KDIAG",kdiag,0)
else
icheckgrad=3
endif
+ call reada(controlcard,'DELTA',aincr,1.0d-7)
elseif (index(controlcard,'THREAD').gt.0) then
modecalc=2
call readi(controlcard,'THREAD',nthread,0)
bordliptop=(boxzsize+lipthick)/2.0
bordlipbot=bordliptop-lipthick
C endif
- if ((bordliptop.gt.boxzsize).or.(borlipbot.lt.0.0))
+ if ((bordliptop.gt.boxzsize).or.(bordlipbot.lt.0.0))
& write(iout,*) "WARNING WRONG SIZE OF LIPIDIC PHASE"
buflipbot=bordlipbot+lipbufthick
bufliptop=bordliptop-lipbufthick
write(iout,*) "bufliptop=",bufliptop
write(iout,*) "buflipbot=",buflipbot
write (iout,*) "SHIELD MODE",shield_mode
+ if (TUBElog.gt.0) then
+ call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+ call reada(controlcard,"YTUBE",tubecenter(2),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
if (shield_mode.gt.0) then
pi=3.141592d0
C VSolvSphere the volume of solving sphere
c call reada(controlcard,"LAMBDA",rlamb,0.3d0)
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
+ tnp = index(controlcard,"NOSEPOINCARE99").gt.0
+ tnp1 = index(controlcard,"NOSEPOINCARE01").gt.0
+ tnh = index(controlcard,"NOSEHOOVER96").gt.0
+ if (RESPA.and.tnh)then
+ xiresp = index(controlcard,"XIRESP").gt.0
+ endif
+ write(iout,*) "tnh",tnh
+ call reada(controlcard,"Q_NP",Q_np,0.1d0)
usampl = index(controlcard,"USAMPL").gt.0
mdpdb = index(controlcard,"MDPDB").gt.0
& "Velocities will be reset at random every",count_reset_vel,
& " steps"
endif
+ else if (tnp .or. tnp1 .or. tnh) then
+ if (tnp .or. tnp1) then
+ write (iout,'(a)') "Nose-Poincare bath calculation"
+ if (tnp) write (iout,'(a)')
+ & "J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird"
+ if (tnp1) write (iout,'(a)') "JPSJ 70 75 (2001) S. Nose"
+ else
+ write (iout,'(a)') "Nose-Hoover bath calculation"
+ write (iout,'(a)') "Mol.Phys. 87 1117 (1996) Martyna et al."
+ nresn=1
+ nyosh=1
+ nnos=1
+ do i=1,nnos
+ qmass(i)=Q_np
+ xlogs(i)=1.0
+ vlogs(i)=0.0
+ enddo
+ do i=1,nyosh
+ WDTI(i) = 1.0*d_time/nresn
+ WDTI2(i)=WDTI(i)/2
+ WDTI4(i)=WDTI(i)/4
+ WDTI8(i)=WDTI(i)/8
+ enddo
+ if (RESPA) then
+ if(xiresp) then
+ write (iout,'(a)') "NVT-XI-RESPA algorithm"
+ else
+ write (iout,'(a)') "NVT-XO-RESPA algorithm"
+ endif
+ do i=1,nyosh
+ WDTIi(i) = 1.0*d_time/nresn/ntime_split
+ WDTIi2(i)=WDTIi(i)/2
+ WDTIi4(i)=WDTIi(i)/4
+ WDTIi8(i)=WDTIi(i)/8
+ enddo
+ endif
+ endif
else
if(me.eq.king.or..not.out1file)
& write (iout,'(a31)') "Microcanonical mode calculation"
include 'COMMON.BOUNDS'
include 'COMMON.MD'
include 'COMMON.SETUP'
+ include 'COMMON.SHIELD'
character*4 sequence(maxres)
integer rescode
double precision x(maxvar)
call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
call reada(weightcard,'TEMP0',temp0,300.0d0)
+ call reada(weightcard,'WSHIELD',wshield,1.0d0)
call reada(weightcard,'WLT',wliptran,0.0D0)
+ call reada(weightcard,'WTUBE',wtube,1.0D0)
if (index(weightcard,'SOFT').gt.0) ipot=6
C 12/1/95 Added weight for the multi-body term WCORR
call reada(weightcard,'WCORRH',wcorr,1.0D0)
call reada(weightcard,"BTRISS",btriss,0.021D0)
call reada(weightcard,"CTRISS",ctriss,1.001D0)
call reada(weightcard,"DTRISS",dtriss,1.001D0)
+ call reada(weightcard,"LIPSCALE",lipscale,1.3D0)
write (iout,*) "ATRISS=", atriss
write (iout,*) "BTRISS=", btriss
write (iout,*) "CTRISS=", ctriss
write (iout,*) "DTRISS=", dtriss
+ if (shield_mode.gt.0) then
+ lipscale=0.0d0
+ write (iout,*) "liscale not used in shield mode"
+ endif
+ write (iout,*) "lipid scaling factor", lipscale
dyn_ss=(index(weightcard,'DYN_SS').gt.0)
do i=1,maxres
dyn_ss_mask(i)=.false.
if (dyn_ss) then
ss_depth=ebr/wsc-0.25*eps(1,1)
Ht=Ht/wsc-0.25*eps(1,1)
- akcm=akcm*wstrain/wsc
- akth=akth*wstrain/wsc
- akct=akct*wstrain/wsc
- v1ss=v1ss*wstrain/wsc
- v2ss=v2ss*wstrain/wsc
- v3ss=v3ss*wstrain/wsc
+ akcm=akcm/wsc
+ akth=akth/wsc
+ akct=akct/wsc
+ v1ss=v1ss/wsc
+ v2ss=v2ss/wsc
+ v3ss=v3ss/wsc
else
if (wstrain.ne.0.0) then
ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
ss_depth=0.0
endif
endif
-
+ write (iout,*) "wshield,", wshield
if(me.eq.king.or..not.out1file) then
write (iout,*) "Parameters of the SS-bond potential:"
write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
call MPI_Finalize(MPI_COMM_WORLD,IERROR)
stop 'Error reading reference structure'
#endif
- 39 call chainbuild
+ 39 call chainbuild_extconf
call setup_var
czscore call geom_to_var(nvar,coord_exp_zs(1,1))
nstart_sup=nnt
return
else
call read_angles(inp,*36)
+ call chainbuild_extconf
endif
goto 37
36 write (iout,'(a)') 'Error reading angle file.'
omeg(i)=-120d0*deg2rad
if (itype(i).le.0) omeg(i)=-omeg(i)
enddo
+ call chainbuild_extconf
else
if(me.eq.king.or..not.out1file)
& write (iout,'(a)') 'Random-generated initial geometry.'
cd write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
cd & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
cd & ' nsup',nsup
+ if (constr_dist.eq.11) then
+ do i=nstart_sup,nstart_sup+nsup-1
+ do j=i+2,nstart_sup+nsup-1
+ distance=dist(i,j)
+ if (distance.le.15.0) then
+ nhpb=nhpb+1
+ ihpb(nhpb)=i+nstart_seq-nstart_sup
+ jhpb(nhpb)=j+nstart_seq-nstart_sup
+ forcon(nhpb)=sqrt(0.04*distance)
+ fordepth(nhpb)=sqrt(40.0/distance)
+ dhpb(nhpb)=distance-0.1d0
+ dhpb1(nhpb)=distance+0.1d0
+
+#ifdef MPI
+ if (.not.out1file .or. me.eq.king)
+ & write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+#else
+ write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ",
+ & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
+#endif
+ endif
+ enddo
+ enddo
+ else
do i=nstart_sup,nstart_sup+nsup-1
cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
cd & ' seq_pdb', restyp(itype_pdb(i))
forcon(nhpb)=weidis
dhpb(nhpb)=dist(i,j)
enddo
- enddo
+ enddo
+ endif
cd write (iout,'(a)') 'Distance constraints:'
cd do i=nss+1,nhpb
cd ii=ihpb(i)
open (itorp,file=torname,status='old',readonly,shared)
call getenv_loc('TORDPAR',tordname)
open (itordp,file=tordname,status='old',readonly,shared)
+ call getenv_loc('TORKCC',torkccname)
+ open (itorkcc,file=torkccname,status='old',readonly,shared)
+ call getenv_loc('THETKCC',thetkccname)
+ open (ithetkcc,file=thetkccname,status='old',readonly,shared)
call getenv_loc('FOURIER',fouriername)
open (ifourier,file=fouriername,status='old',readonly,shared)
call getenv_loc('ELEPAR',elename)
open (ielep,file=elename,status='old',readonly,shared)
call getenv_loc('SIDEPAR',sidename)
open (isidep,file=sidename,status='old',readonly,shared)
+ call getenv_loc('LIPTRANPAR',liptranname)
+ open (iliptranpar,file=liptranname,status='old',readonly,shared)
#elif (defined CRAY) || (defined AIX)
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
& action='read')
c print *,"Processor",myrank," opened file ITORP"
call getenv_loc('TORDPAR',tordname)
open (itordp,file=tordname,status='old',action='read')
+ call getenv_loc('TORKCC',torkccname)
+ open (itorkcc,file=torkccname,status='old',action='read')
+ call getenv_loc('THETKCC',thetkccname)
+ open (ithetkcc,file=thetkccname,status='old',action='read')
c print *,"Processor",myrank," opened file ITORDP"
call getenv_loc('SCCORPAR',sccorname)
open (isccor,file=sccorname,status='old',action='read')
c 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')
c print *,"Processor",myrank," opened file ISIDEP"
c print *,"Processor",myrank," opened parameter files"
#elif (defined G77)
open (itorp,file=torname,status='old')
call getenv_loc('TORDPAR',tordname)
open (itordp,file=tordname,status='old')
+ call getenv_loc('TORKCC',torkccname)
+ open (itorkcc,file=torkccname,status='old')
+ call getenv_loc('THETKCC',thetkccname)
+ open (ithetkcc,file=thetkccname,status='old')
call getenv_loc('SCCORPAR',sccorname)
open (isccor,file=sccorname,status='old')
call getenv_loc('FOURIER',fouriername)
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')
#else
open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
& readonly)
open (itorp,file=torname,status='old',readonly)
call getenv_loc('TORDPAR',tordname)
open (itordp,file=tordname,status='old',readonly)
+ call getenv_loc('TORKCC',torkccname)
+ open (itorkcc,file=torkccname,status='old',readonly)
+ call getenv_loc('THETKCC',thetkccname)
+ open (ithetkcc,file=thetkccname,status='old',readonly)
call getenv_loc('SCCORPAR',sccorname)
open (isccor,file=sccorname,status='old',readonly)
#ifndef CRYST_THETA
open (irotam_pdb,file=rotname_pdb,status='old',action='read')
#endif
#endif
+ call getenv_loc('TUBEPAR',tubename)
+ open (itube,file=tubename,status='old',readonly)
#ifndef OLDSCP
C
C 8/9/01 In the newest version SCp interaction constants are read from a file
write (iout,*) "Calling read_dist_constr"
c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
c call flush(iout)
+ if ((genconstr.gt.0).and.(constr_dist.eq.11)) then
+ call gen_dist_constr
+ go to 1712
+ endif
call card_concat(controlcard)
call readi(controlcard,"NFRAG",nfrag_,0)
call readi(controlcard,"NPAIR",npair_,0)
#endif
enddo
+ 1712 continue
call flush(iout)
return
end
projects / unres.git / blobdiff