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
if (TUBElog.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)
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"
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
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)
iread=index(rekord,lancuch(:ilen(lancuch))//"=")
if (iread.eq.0) return
iread=iread+ilen(lancuch)+1
+
read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
10 return
end
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