2 !-----------------------------------------------------------------------------
11 !-----------------------------------------------------------------------------
14 !-----------------------------------------------------------------------------
18 real(kind=8),dimension(:,:,:),allocatable :: t,r !(3,3,maxres)
19 !-----------------------------------------------------------------------------
22 !-----------------------------------------------------------------------------
24 ! Variables (set in init routine) never modified by local_move
26 integer :: init_called
27 logical :: locmove_output
28 real(kind=8) :: min_theta, max_theta
29 real(kind=8) :: dmin2,dmax2
30 real(kind=8) :: flag,small,small2
31 ! Workspace for local_move
33 integer :: a_n,b_n,res_n
34 real(kind=8),dimension(0:7) :: a_ang
35 real(kind=8),dimension(0:3) :: b_ang
36 real(kind=8),dimension(0:11) :: res_ang
37 logical,dimension(0:2,0:7) :: a_tab
38 logical,dimension(0:2,0:3) :: b_tab
39 logical,dimension(0:2,0:2,0:11) :: res_tab
40 !-----------------------------------------------------------------------------
41 ! integer,dimension(:),allocatable :: itype_pdb !(maxres) initialize in molread
42 !-----------------------------------------------------------------------------
45 !-----------------------------------------------------------------------------
47 !-----------------------------------------------------------------------------
49 !-----------------------------------------------------------------------------
50 real(kind=8) function ARCOS(X)
51 ! implicit real*8 (a-h,o-z)
52 ! include 'COMMON.GEO'
55 IF (DABS(X).LT.1.0D0) GOTO 1
56 ARCOS=PIPOL*(1.0d0-DSIGN(1.0D0,X))
61 !-----------------------------------------------------------------------------
63 !-----------------------------------------------------------------------------
66 ! Build the virtual polypeptide chain. Side-chain centroids are moveable.
69 ! implicit real*8 (a-h,o-z)
70 ! include 'DIMENSIONS'
71 ! include 'COMMON.CHAIN'
72 ! include 'COMMON.LOCAL'
73 ! include 'COMMON.GEO'
74 ! include 'COMMON.VAR'
75 ! include 'COMMON.IOUNITS'
76 ! include 'COMMON.NAMES'
77 ! include 'COMMON.INTERACT'
81 real(kind=8) :: be,be1,alfai
84 ! Set lprn=.true. for debugging
86 print *,"I ENTER CHAINBUILD"
88 ! Define the origin and orientation of the coordinate system and locate the
89 ! first three CA's and SC(2).
91 !elwrite(iout,*)"in chainbuild"
93 !elwrite(iout,*)"after orig_frame"
95 ! Build the alpha-carbon chain.
98 call locate_next_res(i)
100 !elwrite(iout,*)"after locate_next_res"
102 ! First and last SC must coincide with the corresponding CA.
106 dc_norm(j,nres+1)=0.0D0
107 dc(j,nres+nres)=0.0D0
108 dc_norm(j,nres+nres)=0.0D0
110 c(j,nres+nres)=c(j,nres)
113 ! Temporary diagnosis
118 write (iout,'(/a)') 'Recalculated internal coordinates'
121 c(j,nres2+2)=0.5D0*(c(j,i-1)+c(j,i+1)) !maxres2=2*maxres
124 if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
125 be1=rad2deg*beta(nres+i,i,nres2+2,i+1)
127 if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
128 write (iout,1212) restyp(itype(i,1),1),i,dist(i-1,i),&
129 alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,nres2+2),be1
131 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
136 end subroutine chainbuild
137 !-----------------------------------------------------------------------------
138 subroutine orig_frame
140 ! Define the origin and orientation of the coordinate system and locate
141 ! the first three atoms.
143 ! implicit real*8 (a-h,o-z)
144 ! include 'DIMENSIONS'
145 ! include 'COMMON.CHAIN'
146 ! include 'COMMON.LOCAL'
147 ! include 'COMMON.GEO'
148 ! include 'COMMON.VAR'
151 real(kind=8) :: cost,sint
153 !el allocate(t(3,3,nres)) !(3,3,maxres)
154 !el allocate(r(3,3,nres)) !(3,3,maxres)
155 !el allocate(rt(3,3,nres)) !(3,3,maxres)
156 !el allocate(dc_norm(3,0:2*nres)) !(3,0:maxres2)
157 !el allocate(prod(3,3,nres)) !(3,3,maxres)
210 dc_norm(j,2)=prod(j,1,2)
211 dc(j,2)=vbld(3)*prod(j,1,2)
212 c(j,3)=c(j,2)+dc(j,2)
214 call locate_side_chain(2)
216 end subroutine orig_frame
217 !-----------------------------------------------------------------------------
218 subroutine locate_next_res(i)
220 ! Locate CA(i) and SC(i-1)
222 ! implicit real*8 (a-h,o-z)
223 ! include 'DIMENSIONS'
224 ! include 'COMMON.CHAIN'
225 ! include 'COMMON.LOCAL'
226 ! include 'COMMON.GEO'
227 ! include 'COMMON.VAR'
228 ! include 'COMMON.IOUNITS'
229 ! include 'COMMON.NAMES'
230 ! include 'COMMON.INTERACT'
232 ! Define the rotation matrices corresponding to CA(i)
236 real(kind=8) :: theti,phii
237 real(kind=8) :: cost,sint,cosphi,sinphi
242 call proc_proc(theti,icrc)
243 if(icrc.eq.1)theti=100.0
246 call proc_proc(phii,icrc)
247 if(icrc.eq.1)phii=180.0
250 if (theti.ne.theti) theti=100.0
252 if (phii.ne.phii) phii=180.0
262 ! Define the matrices of the rotation about the virtual-bond valence angles
263 ! theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
264 ! program), R(i,j,k), and, the cumulative matrices of rotation RT
286 rt(2,1,i-2)=sint*cosphi
287 rt(2,2,i-2)=-cost*cosphi
289 rt(3,1,i-2)=-sint*sinphi
290 rt(3,2,i-2)=cost*sinphi
292 call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
294 dc_norm(j,i-1)=prod(j,1,i-1)
295 dc(j,i-1)=vbld(i)*prod(j,1,i-1)
296 c(j,i)=c(j,i-1)+dc(j,i-1)
298 !d print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
300 ! Now calculate the coordinates of SC(i-1)
302 call locate_side_chain(i-1)
304 end subroutine locate_next_res
305 !-----------------------------------------------------------------------------
306 subroutine locate_side_chain(i)
308 ! Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
310 ! implicit real*8 (a-h,o-z)
311 ! include 'DIMENSIONS'
312 ! include 'COMMON.CHAIN'
313 ! include 'COMMON.LOCAL'
314 ! include 'COMMON.GEO'
315 ! include 'COMMON.VAR'
316 ! include 'COMMON.IOUNITS'
317 ! include 'COMMON.NAMES'
318 ! include 'COMMON.INTERACT'
320 real(kind=8),dimension(3) :: xx
321 real(kind=8) :: alphi,omegi,theta2
322 real(kind=8) :: dsci,dsci_inv,sinalphi,cosalphi,cosomegi,sinomegi
323 real(kind=8) :: xp,yp,zp,cost2,sint2,rj
324 ! dsci=dsc(itype(i,1))
325 ! dsci_inv=dsc_inv(itype(i,1))
327 dsci_inv=vbld_inv(i+nres)
334 call proc_proc(alphi,icrc)
335 if(icrc.eq.1)alphi=100.0
337 call proc_proc(omegi,icrc)
338 if(icrc.eq.1)omegi=-100.0
340 if (alphi.ne.alphi) alphi=100.0
341 if (omegi.ne.omegi) omegi=-100.0
352 yp= dsci*sinalphi*cosomegi
353 zp=-dsci*sinalphi*sinomegi
354 ! Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
355 ! X-axis aligned with the vector DC(*,i)
356 theta2=pi-0.5D0*theta(i+1)
359 xx(1)= xp*cost2+yp*sint2
360 xx(2)=-xp*sint2+yp*cost2
362 !d print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i,1)),i,
363 !d & xp,yp,zp,(xx(k),k=1,3)
367 ! Bring the SC vectors to the common coordinate system.
369 xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
370 xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
377 rj=rj+prod(j,k,i-1)*xx(k)
380 dc_norm(j,nres+i)=rj*dsci_inv
381 c(j,nres+i)=c(j,i)+rj
384 end subroutine locate_side_chain
385 !-----------------------------------------------------------------------------
387 !-----------------------------------------------------------------------------
388 subroutine int_from_cart1(lprn)
389 ! implicit real*8 (a-h,o-z)
390 ! include 'DIMENSIONS'
395 ! include 'COMMON.IOUNITS'
396 ! include 'COMMON.VAR'
397 ! include 'COMMON.CHAIN'
398 ! include 'COMMON.GEO'
399 ! include 'COMMON.INTERACT'
400 ! include 'COMMON.LOCAL'
401 ! include 'COMMON.NAMES'
402 ! include 'COMMON.SETUP'
403 ! include 'COMMON.TIME1'
407 real(kind=8) :: dnorm1,dnorm2,be
410 if (lprn) write (iout,'(/a)') 'Recalculated internal coordinates'
417 !write(iout,*)"geometry warring, vbld=",(vbld(i),i=1,nres+1)
419 vbld_inv(nres+1)=0.0d0
420 vbld_inv(2*nres)=0.0d0
423 #if defined(PARINT) && defined(MPI)
424 do i=iint_start,iint_end
431 c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))/dnorm1 &
432 +(c(j,i+1)-c(j,i))/dnorm2)
436 if (i.le.nres) phi(i+1)=beta(i-2,i-1,i,i+1)
437 if ((itype(i,1).ne.10).and.(itype(i-1,1).ne.10)) then
438 tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
440 if (itype(i-1,1).ne.10) then
441 tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
442 omicron(1,i)=alpha(i-2,i-1,i-1+nres)
443 omicron(2,i)=alpha(i-1+nres,i-1,i)
445 if (itype(i,1).ne.10) then
446 tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
449 omeg(i)=beta(nres+i,i,nres2+2,i+1)
450 alph(i)=alpha(nres+i,i,nres2+2)
451 theta(i+1)=alpha(i-1,i,i+1)
453 ! print *,i,vbld(i),"vbld(i)"
454 vbld_inv(i)=1.0d0/vbld(i)
455 vbld(nres+i)=dist(nres+i,i)
456 if (itype(i,1).ne.10) then
457 vbld_inv(nres+i)=1.0d0/vbld(nres+i)
459 vbld_inv(nres+i)=0.0d0
462 #if defined(PARINT) && defined(MPI)
463 if (nfgtasks1.gt.1) then
464 !d write(iout,*) "iint_start",iint_start," iint_count",
465 !d & (iint_count(i),i=0,nfgtasks-1)," iint_displ",
466 !d & (iint_displ(i),i=0,nfgtasks-1)
467 !d write (iout,*) "Gather vbld backbone"
470 call MPI_Allgatherv(vbld(iint_start),iint_count(fg_rank1),&
471 MPI_DOUBLE_PRECISION,vbld(1),iint_count(0),iint_displ(0),&
472 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
473 !d write (iout,*) "Gather vbld_inv"
475 call MPI_Allgatherv(vbld_inv(iint_start),iint_count(fg_rank1),&
476 MPI_DOUBLE_PRECISION,vbld_inv(1),iint_count(0),iint_displ(0),&
477 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
478 !d write (iout,*) "Gather vbld side chain"
480 call MPI_Allgatherv(vbld(iint_start+nres),iint_count(fg_rank1),&
481 MPI_DOUBLE_PRECISION,vbld(nres+1),iint_count(0),iint_displ(0),&
482 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
483 !d write (iout,*) "Gather vbld_inv side chain"
485 call MPI_Allgatherv(vbld_inv(iint_start+nres),&
486 iint_count(fg_rank1),MPI_DOUBLE_PRECISION,vbld_inv(nres+1),&
487 iint_count(0),iint_displ(0),MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
488 !d write (iout,*) "Gather theta"
490 call MPI_Allgatherv(theta(iint_start+1),iint_count(fg_rank1),&
491 MPI_DOUBLE_PRECISION,theta(2),iint_count(0),iint_displ(0),&
492 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
493 !d write (iout,*) "Gather phi"
495 call MPI_Allgatherv(phi(iint_start+1),iint_count(fg_rank1),&
496 MPI_DOUBLE_PRECISION,phi(2),iint_count(0),iint_displ(0),&
497 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
499 !d write (iout,*) "Gather alph"
501 call MPI_Allgatherv(alph(iint_start),iint_count(fg_rank1),&
502 MPI_DOUBLE_PRECISION,alph(1),iint_count(0),iint_displ(0),&
503 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
504 !d write (iout,*) "Gather omeg"
506 call MPI_Allgatherv(omeg(iint_start),iint_count(fg_rank1),&
507 MPI_DOUBLE_PRECISION,omeg(1),iint_count(0),iint_displ(0),&
508 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
510 time_gather=time_gather+MPI_Wtime()-time00
516 #if defined(WHAM_RUN) || defined(CLUSTER)
517 dc(j,i)=c(j,i+1)-c(j,i)
519 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
525 #if defined(WHAM_RUN) || defined(CLUSTER)
526 dc(j,i+nres)=c(j,i+nres)-c(j,i)
528 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
533 write (iout,1212) restyp(itype(i,1),1),i,vbld(i),&
534 rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),&
535 rad2deg*alph(i),rad2deg*omeg(i)
538 1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
540 time_intfcart=time_intfcart+MPI_Wtime()-time01
543 end subroutine int_from_cart1
544 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
545 !-----------------------------------------------------------------------------
547 !-----------------------------------------------------------------------------
548 subroutine check_sc_distr
549 ! implicit real*8 (a-h,o-z)
550 ! include 'DIMENSIONS'
551 ! include 'COMMON.TIME1'
552 ! include 'COMMON.INTERACT'
553 ! include 'COMMON.NAMES'
554 ! include 'COMMON.GEO'
555 ! include 'COMMON.HEADER'
556 ! include 'COMMON.CONTROL'
558 real(kind=8),dimension(6*nres) :: varia !(maxvar) (maxvar=6*maxres)
559 real(kind=8) :: hrtime,mintime,sectime
560 integer,parameter :: MaxSample=10000000
561 real(kind=8),parameter :: delt=1.0D0/MaxSample
562 real(kind=8),dimension(0:72,0:90) :: prob
564 integer :: it,i,j,isample,indal,indom
565 real(kind=8) :: al,om,dV
566 dV=2.0D0*5.0D0*deg2rad*deg2rad
569 if ((it.eq.10).or.(it.eq.ntyp1)) goto 10
570 open (20,file=restyp(it,1)//'_distr.sdc',status='unknown')
571 call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
574 open (20,file=restyp(it,1)//'_distr1.sdc',status='unknown')
580 do isample=1,MaxSample
581 call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
583 indom=(rad2deg*om+180.0D0)/5
584 prob(indom,indal)=prob(indom,indal)+delt
588 write (20,'(2f10.3,1pd15.5)') 2*i+0.0D0,5*j-180.0D0,&
594 end subroutine check_sc_distr
596 !-----------------------------------------------------------------------------
598 !-----------------------------------------------------------------------------
599 subroutine geom_to_var(n,x)
601 ! Transfer the geometry parameters to the variable array.
602 ! The positions of variables are as follows:
603 ! 1. Virtual-bond torsional angles: 1 thru nres-3
604 ! 2. Virtual-bond valence angles: nres-2 thru 2*nres-5
605 ! 3. The polar angles alpha of local SC orientation: 2*nres-4 thru
607 ! 4. The torsional angles omega of SC orientation: 2*nres-4+nside+1
608 ! thru 2*nre-4+2*nside
610 ! implicit real*8 (a-h,o-z)
611 ! include 'DIMENSIONS'
612 ! include 'COMMON.VAR'
613 ! include 'COMMON.GEO'
614 ! include 'COMMON.CHAIN'
616 real(kind=8),dimension(n) :: x
617 !d print *,'nres',nres,' nphi',nphi,' ntheta',ntheta,' nvar',nvar
620 !d print *,i,i-3,phi(i)
622 if (n.eq.nphi) return
625 !d print *,i,i-2+nphi,theta(i)
627 if (n.eq.nphi+ntheta) return
629 if (ialph(i,1).gt.0) then
630 x(ialph(i,1))=alph(i)
631 x(ialph(i,1)+nside)=omeg(i)
632 !d print *,i,ialph(i,1),ialph(i,1)+nside,alph(i),omeg(i)
636 end subroutine geom_to_var
637 !-----------------------------------------------------------------------------
638 subroutine var_to_geom(n,x)
640 ! Update geometry parameters according to the variable array.
642 ! implicit real*8 (a-h,o-z)
643 ! include 'DIMENSIONS'
644 ! include 'COMMON.VAR'
645 ! include 'COMMON.CHAIN'
646 ! include 'COMMON.GEO'
647 ! include 'COMMON.IOUNITS'
649 real(kind=8),dimension(n) :: x
650 logical :: change !,reduce
657 if (n.gt.nphi+ntheta) then
660 alph(ii)=x(nphi+ntheta+i)
661 omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
662 !elwrite(iout,*) "alph",ii,alph
663 !elwrite(iout,*) "omeg",ii,omeg
668 !elwrite(iout,*) "phi",i,phi
670 if (n.eq.nphi) return
673 !elwrite(iout,*) "theta",i,theta
674 if (theta(i).eq.pi) theta(i)=0.99d0*pi
678 end subroutine var_to_geom
679 !-----------------------------------------------------------------------------
680 logical function convert_side(alphi,omegi)
682 real(kind=8) :: alphi,omegi
683 !el real(kind=8) :: pinorm
684 ! include 'COMMON.GEO'
686 ! Apply periodicity restrictions.
687 if (alphi.gt.pi) then
689 omegi=pinorm(omegi+pi)
693 end function convert_side
694 !-----------------------------------------------------------------------------
695 logical function reduce(x)
697 ! Apply periodic restrictions to variables.
699 ! implicit real*8 (a-h,o-z)
700 ! include 'DIMENSIONS'
701 ! include 'COMMON.VAR'
702 ! include 'COMMON.CHAIN'
703 ! include 'COMMON.GEO'
704 logical :: zm,zmiana !,convert_side
705 real(kind=8),dimension(nvar) :: x
709 x(i-3)=pinorm(x(i-3))
711 if (nvar.gt.nphi+ntheta) then
715 x(ii)=thetnorm(x(ii))
716 x(iii)=pinorm(x(iii))
717 ! Apply periodic restrictions.
718 zm=convert_side(x(ii),x(iii))
722 if (nvar.eq.nphi) return
726 x(ii)=dmod(x(ii),dwapi)
727 ! Apply periodic restrictions.
728 if (x(ii).gt.pi) then
731 if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
732 if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
735 x(ii)=dmod(pi-x(ii),dwapi)
736 x(ii+nside)=pinorm(-x(ii+nside))
737 zm=convert_side(x(ii),x(ii+nside))
739 else if (x(ii).lt.-pi) then
744 x(ii)=dmod(pi-x(ii),dwapi)
745 x(ii+nside)=pinorm(-pi-x(ii+nside))
746 zm=convert_side(x(ii),x(ii+nside))
748 else if (x(ii).lt.0.0d0) then
751 if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
752 if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
755 x(ii+nside)=pinorm(-x(ii+nside))
756 zm=convert_side(x(ii),x(ii+nside))
763 !-----------------------------------------------------------------------------
764 real(kind=8) function thetnorm(x)
765 ! This function puts x within [0,2Pi].
768 ! include 'COMMON.GEO'
770 if (xx.lt.0.0d0) xx=xx+dwapi
771 if (xx.gt.0.9999d0*pi) xx=0.9999d0*pi
774 end function thetnorm
775 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
776 !-----------------------------------------------------------------------------
777 subroutine var_to_geom_restr(n,xx)
779 ! Update geometry parameters according to the variable array.
781 ! implicit real*8 (a-h,o-z)
782 ! include 'DIMENSIONS'
783 ! include 'COMMON.VAR'
784 ! include 'COMMON.CHAIN'
785 ! include 'COMMON.GEO'
786 ! include 'COMMON.IOUNITS'
788 real(kind=8),dimension(6*nres) :: x,xx !(maxvar) (maxvar=6*maxres)
789 logical :: change !,reduce
795 alph(ii)=x(nphi+ntheta+i)
796 omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
803 if (theta(i).eq.pi) theta(i)=0.99d0*pi
807 end subroutine var_to_geom_restr
808 !-----------------------------------------------------------------------------
810 !-----------------------------------------------------------------------------
811 subroutine gen_rand_conf(nstart,*)
812 ! Generate random conformation or chain cut and regrowth.
814 use random, only: iran_num,ran_number
815 ! implicit real*8 (a-h,o-z)
816 ! include 'DIMENSIONS'
817 ! include 'COMMON.CHAIN'
818 ! include 'COMMON.LOCAL'
819 ! include 'COMMON.VAR'
820 ! include 'COMMON.INTERACT'
821 ! include 'COMMON.IOUNITS'
822 ! include 'COMMON.MCM'
823 ! include 'COMMON.GEO'
824 ! include 'COMMON.CONTROL'
825 logical :: back,fail !overlap,
827 integer :: i,nstart,maxsi,nsi,maxnit,nit,niter
828 integer :: it1,it2,it,j
829 !d print *,' CG Processor',me,' maxgen=',maxgen
831 write (iout,*) 'Gen_Rand_conf: nstart=',nstart,nres
832 if (nstart.lt.5) then
834 phi(4)=gen_phi(4,iabs(itype(2,1)),iabs(itype(3,1)))
835 ! write(iout,*)'phi(4)=',rad2deg*phi(4)
836 if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2,1)),pi,phi(4),molnum(2))
837 ! write(iout,*)'theta(3)=',rad2deg*theta(3)
838 if ((it1.ne.10).and.(it1.ne.ntyp1)) then
841 do while (fail.and.nsi.le.maxsi)
842 call gen_side(it1,theta(3),alph(2),omeg(2),fail,molnum(2))
843 write (iout,*) 'nsi=',nsi,maxsi
846 if (nsi.gt.maxsi) return 1
848 write(iout,*) "before origin_frame"
850 write(iout,*) "after origin_frame"
863 do while (i.le.nres .and. niter.lt.maxgen)
864 write(iout,*) 'i=',i,'back=',back
865 if (i.lt.nstart) then
867 write (iout,'(/80(1h*)/2a/80(1h*))') &
868 'Generation procedure went down to ',&
869 'chain beginning. Cannot continue...'
870 write (*,'(/80(1h*)/2a/80(1h*))') &
871 'Generation procedure went down to ',&
872 'chain beginning. Cannot continue...'
876 it1=iabs(itype(i-1,molnum(i-1)))
877 it2=iabs(itype(i-2,molnum(i-2)))
878 it=iabs(itype(i,molnum(i)))
879 if ((it.eq.ntyp1).and.(it1.eq.ntyp1)) &
880 vbld(i)=ran_number(30.0D0,40.0D0)
881 ! print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,&
882 ! ' nit=',nit,' niter=',niter,' maxgen=',maxgen
883 phi(i+1)=gen_phi(i+1,it1,it)
885 phi(i)=gen_phi(i+1,it2,it1)
886 ! print *,'phi(',i,')=',phi(i)
887 theta(i-1)=gen_theta(it2,phi(i-1),phi(i),molnum(i))
888 ! print *,"theta",theta(i-1),phi(i)
889 if ((it2.ne.10).and.(it2.ne.ntyp1)) then
892 do while (fail.and.nsi.le.maxsi)
893 call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail,molnum(i-2))
896 if (nsi.gt.maxsi) return 1
898 call locate_next_res(i-1)
900 theta(i)=gen_theta(it1,phi(i),phi(i+1),molnum(i))
901 ! write(iout,*) "theta(i),",theta(i)
902 if ((it1.ne.10).and.(it1.ne.ntyp1)) then
905 do while (fail.and.nsi.le.maxsi)
906 call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail,molnum(i))
907 ! write(iout,*)"alpha,omeg(i-1)",alph(i-1),omeg(i-1),i,nsi,maxsi
910 if (nsi.gt.maxsi) return 1
912 call locate_next_res(i)
913 write(iout,*) "overlap,",overlap(i-1)
914 if (overlap(i-1)) then
915 if (nit.lt.maxnit) then
925 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
927 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
932 ! write(iout,*) "tu dochodze"
939 if (niter.ge.maxgen) then
940 write (iout,'(a,2i5)') &
941 'Too many trials in conformation generation',niter,maxgen
942 write (*,'(a,2i5)') &
943 'Too many trials in conformation generation',niter,maxgen
948 c(j,nres+nres)=c(j,nres)
951 end subroutine gen_rand_conf
952 !-----------------------------------------------------------------------------
953 logical function overlap(i)
954 ! implicit real*8 (a-h,o-z)
955 ! include 'DIMENSIONS'
956 ! include 'COMMON.CHAIN'
957 ! include 'COMMON.INTERACT'
958 ! include 'COMMON.FFIELD'
959 integer :: i,j,iti,itj,iteli,itelj,k
960 real(kind=8) :: redfac,rcomp
965 iti=iabs(itype(i,molnum(i)))
966 if (iti.gt.ntyp) return
967 ! Check for SC-SC overlaps.
968 !d print *,'nnt=',nnt,' nct=',nct
970 ! print *, "molnum(j)",j,molnum(j)
971 if (molnum(j).eq.1) then
973 if (itj.eq.ntyp1) cycle
974 if (j.lt.i-1 .or. ipot.ne.4) then
975 rcomp=sigmaii(iti,itj)
980 if (dist(nres+i,nres+j).lt.redfac*rcomp) then
983 ! print *,'overlap, SC-SC: i=',i,' j=',j,
984 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
988 else if (molnum(j).eq.2) then
990 if (dist(nres+i,nres+j).lt.redfac*sigma_nucl(iti,itj)) then
993 ! print *,'overlap, SC-SC: i=',i,' j=',j,
994 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
1001 ! Check for overlaps between the added peptide group and the preceding
1005 ! c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
1006 c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1009 if (molnum(j).ne.1) cycle
1010 itj=iabs(itype(j,1))
1011 !d print *,'overlap, p-Sc: i=',i,' j=',j,
1012 !d & ' dist=',dist(nres+j,maxres2+1)
1013 if (dist(nres+j,nres2+3).lt.4.0D0*redfac) then
1018 ! Check for overlaps between the added side chain and the preceding peptide
1021 if (molnum(j).ne.1) cycle
1023 c(k,nres2+3)=0.5D0*(c(k,j)+c(k,j+1))
1025 !d print *,'overlap, SC-p: i=',i,' j=',j,
1026 !d & ' dist=',dist(nres+i,maxres2+1)
1027 if (dist(nres+i,nres2+3).lt.4.0D0*redfac) then
1032 ! Check for p-p overlaps
1034 c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1037 ! if (molnum(j).eq.1) then
1040 c(k,nres2+4)=0.5D0*(c(k,j)+c(k,j+1))
1042 !d print *,'overlap, p-p: i=',i,' j=',j,
1043 !d & ' dist=',dist(maxres2+1,maxres2+2)
1044 if (molnum(j).eq.1) then
1045 if(iteli.ne.0.and.itelj.ne.0)then
1046 if (dist(nres2+3,nres2+4).lt.rpp(iteli,itelj)*redfac) then
1051 else if (molnum(j).eq.2) then
1052 if (dist(nres2+3,nres2+4).lt.3.0) then
1059 end function overlap
1060 !-----------------------------------------------------------------------------
1061 real(kind=8) function gen_phi(i,it1,it2)
1062 use random, only:ran_number
1063 ! implicit real*8 (a-h,o-z)
1064 ! include 'DIMENSIONS'
1065 ! include 'COMMON.GEO'
1066 ! include 'COMMON.BOUNDS'
1067 integer :: i,it1,it2
1068 ! gen_phi=ran_number(-pi,pi)
1069 ! 8/13/98 Generate phi using pre-defined boundaries
1070 gen_phi=ran_number(phibound(1,i),phibound(2,i))
1072 end function gen_phi
1073 !-----------------------------------------------------------------------------
1074 real(kind=8) function gen_theta(it,gama,gama1,mnum)
1075 use random,only:binorm,ran_number
1076 ! implicit real*8 (a-h,o-z)
1077 ! include 'DIMENSIONS'
1078 ! include 'COMMON.LOCAL'
1079 ! include 'COMMON.GEO'
1080 real(kind=8),dimension(2) :: y,z
1081 real(kind=8) :: theta_max,theta_min,sig,ak
1083 integer :: j,it,k,mnum
1084 real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1085 ! print *,'gen_theta: it=',it
1088 if (dabs(gama).gt.dwapi) then
1095 if (dabs(gama1).gt.dwapi) then
1102 if (it.eq.ntyp1) then
1103 gen_theta=ran_number(theta_max/2.0,theta_max)
1104 else if (mnum.eq.1) then
1106 thet_pred_mean=a0thet(it)
1107 ! write(iout,*),it,thet_pred_mean,"gen_thet"
1109 thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1110 +bthet(k,it,1,1)*z(k)
1114 sig=sig*thet_pred_mean+polthet(j,it)
1116 sig=0.5D0/(sig*sig+sigc0(it))
1117 ak=dexp(gthet(1,it)- &
1118 0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1119 ! print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1120 ! print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1121 theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1122 if (theta_temp.lt.theta_min) theta_temp=theta_min
1123 if (theta_temp.gt.theta_max) theta_temp=theta_max
1124 gen_theta=theta_temp
1125 ! print '(a)','Exiting GENTHETA.'
1126 else if (mnum.eq.2) then
1127 gen_theta=2.0d0 + ran_number(0.0d0,0.34d0)
1129 gen_theta=ran_number(theta_max/2.0,theta_max)
1132 end function gen_theta
1133 !-----------------------------------------------------------------------------
1134 subroutine gen_side(it,the,al,om,fail,mnum)
1135 use random, only:ran_number,mult_norm1
1136 ! implicit real*8 (a-h,o-z)
1137 ! include 'DIMENSIONS'
1138 ! include 'COMMON.GEO'
1139 ! include 'COMMON.LOCAL'
1140 ! include 'COMMON.SETUP'
1141 ! include 'COMMON.IOUNITS'
1142 real(kind=8) :: MaxBoxLen=10.0D0
1143 real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1144 real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1145 real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1146 real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1147 real(kind=8),dimension(2) :: y,cm,eig
1148 real(kind=8),dimension(2,2) :: box
1149 real(kind=8),dimension(100) :: work
1150 real(kind=8) :: eig_limit=1.0D-8
1151 real(kind=8) :: Big=10.0D0
1152 logical :: lprint,fail,lcheck
1154 integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob,mnum
1155 real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1156 real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1157 real(kind=8) :: which_lobe
1162 if (the.eq.0.0D0 .or. the.eq.pi) then
1164 write (*,'(a,i4,a,i3,a,1pe14.5)') &
1165 'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1167 !d write (iout,'(a,i3,a,1pe14.5)')
1168 !d & 'Error in GenSide: it=',it,' theta=',the
1173 if (nlobit.eq.0) then
1174 al=ran_number(0.05d0,pi/6)
1175 om=ran_number(-pi,pi)
1178 tant=dtan(the-pipol)
1180 allocate(z(3,nlobit))
1181 allocate(W1(nlobit))
1182 allocate(detAp(nlobit))
1183 allocate(sumW(0:nlobit))
1186 print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1187 write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1189 print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1190 write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1194 zz1=tant-censc(1,i,it)
1197 a(k,l)=gaussc(k,l,i,it)
1200 detApi=a(2,2)*a(3,3)-a(2,3)**2
1201 Ap_inv(2,2)=a(3,3)/detApi
1202 Ap_inv(2,3)=-a(2,3)/detApi
1203 Ap_inv(3,2)=Ap_inv(2,3)
1204 Ap_inv(3,3)=a(2,2)/detApi
1206 write (*,'(/a,i2/)') 'Cluster #',i
1207 write (*,'(3(1pe14.5),5x,1pe14.5)') &
1208 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1209 write (iout,'(/a,i2/)') 'Cluster #',i
1210 write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1211 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1216 W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1220 W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1221 ! if (lprint) write(*,'(a,3(1pe15.5)/)')
1222 ! & 'detAp, W1, anormi',detApi,W1i,anormi
1226 zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1230 detAp(i)=dsqrt(detApi)
1234 print *,'W1:',(w1(i),i=1,nlobit)
1235 print *,'detAp:',(detAp(i),i=1,nlobit)
1238 print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1240 write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1241 write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1244 write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1248 ! Writing the distribution just to check the procedure
1250 dV=deg2rad**2*10.0D0
1254 fac=fac+W1(i)/detAp(i)
1256 fac=1.0D0/(2.0D0*fac*pi)
1257 !d print *,it,'fac=',fac
1266 a(j-1,k-1)=gaussc(j,k,i,it)
1278 wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1281 wart=wart+W1(i)*dexp(-0.5D0*wykl)
1288 ! print *,'y',y(1),y(2),' fac=',fac
1290 write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1295 ! print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1299 ! Calculate the CM of the system
1302 W1(i)=W1(i)/detAp(i)
1306 sumW(i)=sumW(i-1)+W1(i)
1311 cm(1)=cm(1)+z(2,j)*W1(j)
1312 cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1314 cm(1)=cm(1)/sumW(nlobit)
1315 cm(2)=cm(2)/sumW(nlobit)
1316 if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1317 cm(2).gt.Big .or. cm(2).lt.-Big) then
1318 !d write (iout,'(a)')
1319 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1320 !d write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1322 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1323 !d write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1327 !d print *,'CM:',cm(1),cm(2)
1329 ! Find the largest search distance from CM
1335 a(j-1,k-1)=gaussc(j,k,i,it)
1339 call f02faf('N','U',2,a,3,eig,work,100,ifail)
1341 call djacob(2,3,10000,1.0d-10,a,vec,eig)
1345 print *,'*************** CG Processor',me
1346 print *,'CM:',cm(1),cm(2)
1347 write (iout,*) '*************** CG Processor',me
1348 write (iout,*) 'CM:',cm(1),cm(2)
1349 print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1350 write (iout,'(A,8f10.5)') &
1351 'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1354 if (eig(1).lt.eig_limit) then
1356 'From Mult_Norm: Eigenvalues of A are too small.'
1358 'From Mult_Norm: Eigenvalues of A are too small.'
1365 radius=radius+pinorm(z(j+1,i)-cm(j))**2
1367 radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1368 if (radius.gt.radmax) radmax=radius
1370 if (radmax.gt.pi) radmax=pi
1372 ! Determine the boundaries of the search rectangle.
1375 print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1376 print '(a,4(1pe14.4))','radmax: ',radmax
1378 box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1379 box(2,1)=dmin1(cm(1)+radmax,pi)
1380 box(1,2)=cm(2)-radmax
1381 box(2,2)=cm(2)+radmax
1384 print *,'CG Processor',me,' Array BOX:'
1386 print *,'Array BOX:'
1388 print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1389 print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1391 write (iout,*)'CG Processor',me,' Array BOX:'
1393 write (iout,*)'Array BOX:'
1395 write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1396 write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1398 ! if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1400 ! write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1401 ! write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1403 ! write (iout,'(a)') 'Bad sampling box.'
1408 which_lobe=ran_number(0.0D0,sumW(nlobit))
1409 ! print '(a,1pe14.4)','which_lobe=',which_lobe
1411 if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1414 ! print *,'ilob=',ilob,' nlob=',nlob(it)
1418 a(i-1,j-1)=gaussc(i,j,ilob,it)
1421 !d print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1422 call mult_norm1(3,2,a,cm,box,y,fail)
1426 else if (mnum.eq.2) then
1427 al=0.7+ran_number(0.0d0,0.2d0)
1428 om=ran_number(0.0d0,3.14d0)
1431 !d print *,'al=',al,' om=',om
1434 end subroutine gen_side
1435 !-----------------------------------------------------------------------------
1436 subroutine overlap_sc(scfail)
1438 ! Internal and cartesian coordinates must be consistent as input,
1439 ! and will be up-to-date on return.
1440 ! At the end of this procedure, scfail is true if there are
1441 ! overlapping residues left, or false otherwise (success)
1443 ! implicit real*8 (a-h,o-z)
1444 ! include 'DIMENSIONS'
1445 ! include 'COMMON.CHAIN'
1446 ! include 'COMMON.INTERACT'
1447 ! include 'COMMON.FFIELD'
1448 ! include 'COMMON.VAR'
1449 ! include 'COMMON.SBRIDGE'
1450 ! include 'COMMON.IOUNITS'
1451 logical :: had_overlaps,fail,scfail
1452 integer,dimension(nres) :: ioverlap !(maxres)
1453 integer :: ioverlap_last,k,maxsi,i,iti,nsi
1456 had_overlaps=.false.
1457 call overlap_sc_list(ioverlap,ioverlap_last)
1458 if (ioverlap_last.gt.0) then
1459 write (iout,*) '#OVERLAPing residues ',ioverlap_last
1460 write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1466 if (ioverlap_last.eq.0) exit
1468 do ires=1,ioverlap_last
1470 iti=iabs(itype(i,1))
1471 if ((iti.ne.10).and.(molnum(i).ne.5).and.(iti.ne.ntyp1)) then
1474 do while (fail.and.nsi.le.maxsi)
1475 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1483 call overlap_sc_list(ioverlap,ioverlap_last)
1484 ! write (iout,*) 'Overlaping residues ',ioverlap_last,
1485 ! & (ioverlap(j),j=1,ioverlap_last)
1488 if (k.le.1000.and.ioverlap_last.eq.0) then
1490 if (had_overlaps) then
1491 write (iout,*) '#OVERLAPing all corrected after ',k,&
1492 ' random generation'
1496 write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1497 write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1503 write (iout,'(a30,i5,a12,i4)') &
1504 '#OVERLAP FAIL in gen_side after',maxsi,&
1508 end subroutine overlap_sc
1509 !-----------------------------------------------------------------------------
1510 subroutine overlap_sc_list(ioverlap,ioverlap_last)
1512 ! implicit real*8 (a-h,o-z)
1513 ! include 'DIMENSIONS'
1514 ! include 'COMMON.GEO'
1515 ! include 'COMMON.LOCAL'
1516 ! include 'COMMON.IOUNITS'
1517 ! include 'COMMON.CHAIN'
1518 ! include 'COMMON.INTERACT'
1519 ! include 'COMMON.FFIELD'
1520 ! include 'COMMON.VAR'
1521 ! include 'COMMON.CALC'
1523 integer,dimension(nres) :: ioverlap !(maxres)
1524 integer :: ioverlap_last
1527 real(kind=8) :: redfac,sig !rrij,sigsq,
1528 integer :: itypi,itypj,itypi1
1529 real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1533 ! Check for SC-SC overlaps and mark residues
1534 ! print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1536 do i=iatsc_s,iatsc_e
1537 if (itype(i,molnum(i)).eq.ntyp1_molec(molnum(i))) cycle
1538 if (molnum(i).eq.5) print *,"WTF",i,iatsc_s,iatsc_e
1539 if (molnum(i).eq.5) cycle
1540 itypi=iabs(itype(i,molnum(i)))
1541 itypi1=iabs(itype(i+1,1))
1545 dxi=dc_norm(1,nres+i)
1546 dyi=dc_norm(2,nres+i)
1547 dzi=dc_norm(3,nres+i)
1548 dsci_inv=dsc_inv(itypi)
1550 do iint=1,nint_gr(i)
1551 do j=istart(i,iint),iend(i,iint)
1552 if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
1554 itypj=iabs(itype(j,molnum(j)))
1555 dscj_inv=dsc_inv(itypj)
1556 sig0ij=sigma(itypi,itypj)
1557 chi1=chi(itypi,itypj)
1558 chi2=chi(itypj,itypi)
1565 alf12=0.5D0*(alf1+alf2)
1567 rcomp=sigmaii(itypi,itypj)
1569 rcomp=sigma(itypi,itypj)
1571 ! print '(2(a3,2i3),a3,2f10.5)',
1572 ! & ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1577 dxj=dc_norm(1,nres+j)
1578 dyj=dc_norm(2,nres+j)
1579 dzj=dc_norm(3,nres+j)
1580 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1584 sig=sig0ij*dsqrt(sigsq)
1585 rij_shift=1.0D0/rij-sig+sig0ij
1587 !t if ( 1.0/rij .lt. redfac*rcomp .or.
1588 !t & rij_shift.le.0.0D0 ) then
1589 if ( rij_shift.le.0.0D0 ) then
1590 !d write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1591 !d & 'overlap SC-SC: i=',i,' j=',j,
1592 !d & ' dist=',dist(nres+i,nres+j),' rcomp=',
1593 !d & rcomp,1.0/rij,rij_shift
1594 ioverlap_last=ioverlap_last+1
1595 ioverlap(ioverlap_last)=i
1596 do k=1,ioverlap_last-1
1597 if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1599 ioverlap_last=ioverlap_last+1
1600 ioverlap(ioverlap_last)=j
1601 do k=1,ioverlap_last-1
1602 if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1609 end subroutine overlap_sc_list
1611 !-----------------------------------------------------------------------------
1612 ! energy_p_new_barrier.F
1613 !-----------------------------------------------------------------------------
1614 subroutine sc_angular
1615 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1616 ! om12. Called by ebp, egb, and egbv.
1619 ! include 'COMMON.CALC'
1620 ! include 'COMMON.IOUNITS'
1624 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1625 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1626 om12=dxi*dxj+dyi*dyj+dzi*dzj
1628 ! Calculate eps1(om12) and its derivative in om12
1629 faceps1=1.0D0-om12*chiom12
1630 faceps1_inv=1.0D0/faceps1
1631 eps1=dsqrt(faceps1_inv)
1632 ! Following variable is eps1*deps1/dom12
1633 eps1_om12=faceps1_inv*chiom12
1638 ! write (iout,*) "om12",om12," eps1",eps1
1639 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1644 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1645 sigsq=1.0D0-facsig*faceps1_inv
1646 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1647 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1648 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1654 ! write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1655 ! write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1657 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1660 chipom12=chip12*om12
1661 facp=1.0D0-om12*chipom12
1663 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1664 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1665 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1666 ! Following variable is the square root of eps2
1667 eps2rt=1.0D0-facp1*facp_inv
1668 ! Following three variables are the derivatives of the square root of eps
1669 ! in om1, om2, and om12.
1670 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1671 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1672 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1673 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1674 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1675 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1676 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1677 ! & " eps2rt_om12",eps2rt_om12
1678 ! Calculate whole angle-dependent part of epsilon and contributions
1679 ! to its derivatives
1681 end subroutine sc_angular
1682 !-----------------------------------------------------------------------------
1684 subroutine sc_angular_nucl
1685 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1686 ! om12. Called by ebp, egb, and egbv.
1689 ! include 'COMMON.CALC'
1690 ! include 'COMMON.IOUNITS'
1696 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1697 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1698 om12=dxi*dxj+dyi*dyj+dzi*dzj
1700 ! Calculate eps1(om12) and its derivative in om12
1701 faceps1=1.0D0-om12*chiom12
1702 faceps1_inv=1.0D0/faceps1
1703 eps1=dsqrt(faceps1_inv)
1704 ! Following variable is eps1*deps1/dom12
1705 eps1_om12=faceps1_inv*chiom12
1710 ! write (iout,*) "om12",om12," eps1",eps1
1711 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1716 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1717 sigsq=1.0D0-facsig*faceps1_inv
1718 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1719 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1720 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1723 chipom12=chip12*om12
1724 facp=1.0D0-om12*chipom12
1726 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1727 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1728 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1729 ! Following variable is the square root of eps2
1730 eps2rt=1.0D0-facp1*facp_inv
1731 ! Following three variables are the derivatives of the square root of eps
1732 ! in om1, om2, and om12.
1733 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1734 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1735 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1736 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1737 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1738 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1739 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1740 ! & " eps2rt_om12",eps2rt_om12
1741 ! Calculate whole angle-dependent part of epsilon and contributions
1742 ! to its derivatives
1744 end subroutine sc_angular_nucl
1746 !-----------------------------------------------------------------------------
1747 subroutine int_bounds(total_ints,lower_bound,upper_bound)
1748 ! implicit real*8 (a-h,o-z)
1749 ! include 'DIMENSIONS'
1751 ! include 'COMMON.SETUP'
1752 integer :: total_ints,lower_bound,upper_bound,nint
1753 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1754 integer :: i,nexcess
1755 nint=total_ints/nfgtasks
1759 nexcess=total_ints-nint*nfgtasks
1761 int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1765 lower_bound=lower_bound+int4proc(i)
1767 upper_bound=lower_bound+int4proc(fg_rank)
1768 lower_bound=lower_bound+1
1770 end subroutine int_bounds
1771 !-----------------------------------------------------------------------------
1772 subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1773 ! implicit real*8 (a-h,o-z)
1774 ! include 'DIMENSIONS'
1776 ! include 'COMMON.SETUP'
1777 integer :: total_ints,lower_bound,upper_bound,nint
1778 integer :: nexcess,i
1779 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1780 nint=total_ints/nfgtasks1
1784 nexcess=total_ints-nint*nfgtasks1
1786 int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1790 lower_bound=lower_bound+int4proc(i)
1792 upper_bound=lower_bound+int4proc(fg_rank1)
1793 lower_bound=lower_bound+1
1795 end subroutine int_bounds1
1796 !-----------------------------------------------------------------------------
1798 !-----------------------------------------------------------------------------
1799 subroutine chainbuild_cart
1800 ! implicit real*8 (a-h,o-z)
1801 ! include 'DIMENSIONS'
1806 ! include 'COMMON.SETUP'
1807 ! include 'COMMON.CHAIN'
1808 ! include 'COMMON.LOCAL'
1809 ! include 'COMMON.TIME1'
1810 ! include 'COMMON.IOUNITS'
1811 integer :: j,i,ierror,ierr
1812 real(kind=8) :: time00,time01
1814 if (nfgtasks.gt.1) then
1815 ! write (iout,*) "BCAST in chainbuild_cart"
1817 ! Broadcast the order to build the chain and compute internal coordinates
1818 ! to the slaves. The slaves receive the order in ERGASTULUM.
1820 ! write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1822 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1823 ! & (dc(j,i+nres),j=1,3)
1826 call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1827 time_bcast7=time_bcast7+MPI_Wtime()-time00
1829 call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1831 ! write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1833 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1834 ! & (dc(j,i+nres),j=1,3)
1836 ! write (iout,*) "End BCAST in chainbuild_cart"
1838 time_bcast=time_bcast+MPI_Wtime()-time00
1839 time_bcastc=time_bcastc+MPI_Wtime()-time01
1847 c(j,i)=c(j,i-1)+dc(j,i-1)
1852 c(j,i+nres)=c(j,i)+dc(j,i+nres)
1855 ! write (iout,*) "CHAINBUILD_CART"
1857 call int_from_cart1(.false.)
1859 end subroutine chainbuild_cart
1860 !-----------------------------------------------------------------------------
1862 !-----------------------------------------------------------------------------
1863 real(kind=8) function alpha(i1,i2,i3)
1865 ! Calculates the planar angle between atoms (i1), (i2), and (i3).
1867 ! implicit real*8 (a-h,o-z)
1868 ! include 'DIMENSIONS'
1869 ! include 'COMMON.GEO'
1870 ! include 'COMMON.CHAIN'
1873 real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1880 vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1881 wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1882 scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1886 !-----------------------------------------------------------------------------
1887 real(kind=8) function beta(i1,i2,i3,i4)
1889 ! Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1891 ! implicit real*8 (a-h,o-z)
1892 ! include 'DIMENSIONS'
1893 ! include 'COMMON.GEO'
1894 ! include 'COMMON.CHAIN'
1896 integer :: i1,i2,i3,i4
1897 real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1898 real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1899 real(kind=8) :: tx,ty,tz
1909 !d print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1910 !d print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1911 !d print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1915 wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1919 vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1920 if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1921 scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1922 if (dabs(scalar).gt.1.0D0) &
1923 scalar=0.99999999999999D0*scalar/dabs(scalar)
1925 !d print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1930 ! if (angle.le.0.0D0) angle=pi+angle
1934 scalar=tx*x23+ty*y23+tz*z23
1935 if (scalar.lt.0.0D0) angle=-angle
1939 !-----------------------------------------------------------------------------
1940 real(kind=8) function dist(i1,i2)
1942 ! Calculates the distance between atoms (i1) and (i2).
1944 ! implicit real*8 (a-h,o-z)
1945 ! include 'DIMENSIONS'
1946 ! include 'COMMON.GEO'
1947 ! include 'COMMON.CHAIN'
1950 real(kind=8) :: x12,y12,z12
1954 dist=dsqrt(x12*x12+y12*y12+z12*z12)
1957 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1958 !-----------------------------------------------------------------------------
1960 !-----------------------------------------------------------------------------
1961 subroutine local_move_init(debug)
1965 ! implicit real*8 (a-h,o-z)
1966 ! include 'DIMENSIONS' ! Needed by COMMON.LOCAL
1967 ! include 'COMMON.GEO' ! For pi, deg2rad
1968 ! include 'COMMON.LOCAL' ! For vbl
1969 ! include 'COMMON.LOCMOVE'
1975 ! Determine wheter to do some debugging output
1976 locmove_output=debug
1978 ! Set the init_called flag to 1
1981 ! The following are never changed
1982 min_theta=60.D0*deg2rad ! (0,PI)
1983 max_theta=175.D0*deg2rad ! (0,PI)
1984 dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1985 dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1988 small2=0.5*small*small
1990 ! Not really necessary...
1996 end subroutine local_move_init
1997 !-----------------------------------------------------------------------------
1998 subroutine local_move(n_start, n_end, PHImin, PHImax)
1999 ! Perform a local move between residues m and n (inclusive)
2000 ! PHImin and PHImax [0,PI] determine the size of the move
2001 ! Works on whatever structure is in the variables theta and phi,
2002 ! sidechain variables are left untouched
2003 ! The final structure is NOT minimized, but both the cartesian
2004 ! variables c and the angles are up-to-date at the end (no further
2005 ! chainbuild is required)
2007 use random,only:ran_number
2009 ! implicit real*8 (a-h,o-z)
2010 ! include 'DIMENSIONS'
2011 ! include 'COMMON.GEO'
2012 ! include 'COMMON.CHAIN'
2013 ! include 'COMMON.VAR'
2014 ! include 'COMMON.MINIM'
2015 ! include 'COMMON.SBRIDGE'
2016 ! include 'COMMON.LOCMOVE'
2018 ! External functions
2019 !EL integer move_res
2020 !EL external move_res
2021 !EL double precision ran_number
2022 !EL external ran_number
2025 integer :: n_start, n_end ! First and last residues to move
2026 real(kind=8) :: PHImin, PHImax ! min/max angles [0,PI]
2030 real(kind=8) :: min,max
2034 ! Check if local_move_init was called. This assumes that it
2035 ! would not be 1 if not explicitely initialized
2036 if (init_called.ne.1) then
2037 write(6,*)' *** local_move_init not called!!!'
2041 ! Quick check for crazy range
2042 if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2043 write(6,'(a,i3,a,i3)') &
2044 ' *** Cannot make local move between n_start = ',&
2045 n_start,' and n_end = ',n_end
2049 ! Take care of end residues first...
2050 if (n_start.eq.1) then
2051 ! Move residue 1 (completely random)
2052 theta(3)=ran_number(min_theta,max_theta)
2053 phi(4)=ran_number(-PI,PI)
2058 if (n_end.eq.nres) then
2059 ! Move residue nres (completely random)
2060 theta(nres)=ran_number(min_theta,max_theta)
2061 phi(nres)=ran_number(-PI,PI)
2067 ! ...then go through all other residues one by one
2068 ! Start from the two extremes and converge
2073 !$$$c Move the first two residues by less than the others
2074 !$$$ if (i-n_start.lt.3) then
2075 !$$$ if (i-n_start.eq.0) then
2078 !$$$ else if (i-n_start.eq.1) then
2081 !$$$ else if (i-n_start.eq.2) then
2087 ! The actual move, on residue i
2088 iretcode=move_res(min,max,i) ! Discard iretcode
2094 !$$$c Move the last two residues by less than the others
2095 !$$$ if (n_end-j.lt.3) then
2096 !$$$ if (n_end-j.eq.0) then
2099 !$$$ else if (n_end-j.eq.1) then
2102 !$$$ else if (n_end-j.eq.2) then
2108 ! The actual move, on residue j
2109 iretcode=move_res(min,max,j) ! Discard iretcode
2114 call int_from_cart(.false.,.false.)
2117 end subroutine local_move
2118 !-----------------------------------------------------------------------------
2119 subroutine output_tabs
2120 ! Prints out the contents of a_..., b_..., res_...
2124 ! include 'COMMON.GEO'
2125 ! include 'COMMON.LOCMOVE'
2131 write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2132 write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2135 write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2136 write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2139 write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2140 write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2141 write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2142 write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2145 end subroutine output_tabs
2146 !-----------------------------------------------------------------------------
2147 subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2148 ! Only uses angles if [0,PI] (but PHImin cannot be 0.,
2149 ! and PHImax cannot be PI)
2153 ! include 'COMMON.GEO'
2156 real(kind=8) :: PHImin,PHImax
2160 real(kind=8),dimension(0:3) :: ang
2161 logical,dimension(0:2,0:3) :: tab
2164 if (PHImin .eq. PHImax) then
2165 ! Special case with two 010's
2175 else if (PHImin .eq. PI) then
2176 ! Special case with one 010
2182 else if (PHImax .eq. 0.) then
2183 ! Special case with one 010
2192 if (PHImin .gt. 0.) then
2193 ! Start of range (011)
2198 ! End of range (110)
2202 tab(2,n+1) = .false.
2205 if (PHImax .lt. PI) then
2206 ! Start of range (011)
2211 ! End of range (110)
2215 tab(2,n+1) = .false.
2221 end subroutine angles2tab
2222 !-----------------------------------------------------------------------------
2223 subroutine minmax_angles(x,y,z,r,n,ang,tab)
2224 ! When solutions do not exist, assume all angles
2225 ! are acceptable - i.e., initial geometry must be correct
2229 ! include 'COMMON.GEO'
2230 ! include 'COMMON.LOCMOVE'
2233 real(kind=8) :: x,y,z,r
2237 real(kind=8),dimension(0:3) :: ang
2238 logical,dimension(0:2,0:3) :: tab
2241 real(kind=8) :: num, denom, phi
2242 real(kind=8) :: Kmin, Kmax
2246 num = x*x + y*y + z*z
2249 if (denom .gt. 0.) then
2251 denom = 2.*r*sqrt(denom)
2253 Kmin = (num - dmin2)/denom
2254 Kmax = (num - dmax2)/denom
2256 ! Allowed values of K (else all angles are acceptable)
2259 if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2261 else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2267 if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2269 else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2275 if (Kmax .lt. Kmin) Kmax = Kmin
2277 call angles2tab(Kmin, Kmax, n, ang, tab)
2279 ! Add phi and check that angles are within range (-PI,PI]
2282 if (ang(i) .le. -PI) then
2283 ang(i) = ang(i)+2.*PI
2284 else if (ang(i) .gt. PI) then
2285 ang(i) = ang(i)-2.*PI
2291 end subroutine minmax_angles
2292 !-----------------------------------------------------------------------------
2293 subroutine construct_tab
2294 ! Take a_... and b_... values and produces the results res_...
2295 ! x_ang are assumed to be all different (diff > small)
2296 ! x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2300 ! include 'COMMON.LOCMOVE'
2303 integer :: n_max,i,j,index
2309 if (n_max .eq. 0) then
2316 res_tab(j,0,i) = .true.
2317 res_tab(j,2,i) = .true.
2318 res_tab(j,1,i) = .false.
2325 do while (.not.done)
2326 res_ang(index) = flag
2330 if ((a_ang(i)-phi).gt.small .and. &
2331 a_ang(i) .lt. res_ang(index)) then
2332 ! Found a lower angle
2333 res_ang(index) = a_ang(i)
2334 ! Copy the values from a_tab into res_tab(0,,)
2335 res_tab(0,0,index) = a_tab(0,i)
2336 res_tab(0,1,index) = a_tab(1,i)
2337 res_tab(0,2,index) = a_tab(2,i)
2338 ! Set default values for res_tab(1,,)
2339 res_tab(1,0,index) = .true.
2340 res_tab(1,1,index) = .false.
2341 res_tab(1,2,index) = .true.
2342 else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2343 ! Found an equal angle (can only be equal to a b_ang)
2344 res_tab(0,0,index) = a_tab(0,i)
2345 res_tab(0,1,index) = a_tab(1,i)
2346 res_tab(0,2,index) = a_tab(2,i)
2351 if ((b_ang(i)-phi).gt.small .and. &
2352 b_ang(i) .lt. res_ang(index)) then
2353 ! Found a lower angle
2354 res_ang(index) = b_ang(i)
2355 ! Copy the values from b_tab into res_tab(1,,)
2356 res_tab(1,0,index) = b_tab(0,i)
2357 res_tab(1,1,index) = b_tab(1,i)
2358 res_tab(1,2,index) = b_tab(2,i)
2359 ! Set default values for res_tab(0,,)
2360 res_tab(0,0,index) = .true.
2361 res_tab(0,1,index) = .false.
2362 res_tab(0,2,index) = .true.
2363 else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2364 ! Found an equal angle (can only be equal to an a_ang)
2365 res_tab(1,0,index) = b_tab(0,i)
2366 res_tab(1,1,index) = b_tab(1,i)
2367 res_tab(1,2,index) = b_tab(2,i)
2371 if (res_ang(index) .eq. flag) then
2374 else if (index .eq. n_max-1) then
2378 phi = res_ang(index) ! Store previous angle
2386 if (a_n .gt. 0) then
2387 do while (.not.res_tab(0,1,index))
2390 done = res_tab(0,2,index)
2391 do i=index+1,res_n-1
2392 if (res_tab(0,1,i)) then
2393 done = res_tab(0,2,i)
2395 res_tab(0,0,i) = done
2396 res_tab(0,1,i) = done
2397 res_tab(0,2,i) = done
2400 done = res_tab(0,0,index)
2402 if (res_tab(0,1,i)) then
2403 done = res_tab(0,0,i)
2405 res_tab(0,0,i) = done
2406 res_tab(0,1,i) = done
2407 res_tab(0,2,i) = done
2412 res_tab(0,0,i) = .true.
2413 res_tab(0,1,i) = .true.
2414 res_tab(0,2,i) = .true.
2419 if (b_n .gt. 0) then
2420 do while (.not.res_tab(1,1,index))
2423 done = res_tab(1,2,index)
2424 do i=index+1,res_n-1
2425 if (res_tab(1,1,i)) then
2426 done = res_tab(1,2,i)
2428 res_tab(1,0,i) = done
2429 res_tab(1,1,i) = done
2430 res_tab(1,2,i) = done
2433 done = res_tab(1,0,index)
2435 if (res_tab(1,1,i)) then
2436 done = res_tab(1,0,i)
2438 res_tab(1,0,i) = done
2439 res_tab(1,1,i) = done
2440 res_tab(1,2,i) = done
2445 res_tab(1,0,i) = .true.
2446 res_tab(1,1,i) = .true.
2447 res_tab(1,2,i) = .true.
2451 ! Finally fill the last row with AND operation
2454 res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2459 end subroutine construct_tab
2460 !-----------------------------------------------------------------------------
2461 subroutine construct_ranges(phi_n,phi_start,phi_end)
2462 ! Given the data in res_..., construct a table of
2463 ! min/max allowed angles
2467 ! include 'COMMON.GEO'
2468 ! include 'COMMON.LOCMOVE'
2472 real(kind=8),dimension(0:11) :: phi_start,phi_end
2479 if (res_n .eq. 0) then
2480 ! Any move is allowed
2488 do while (.not.done)
2489 ! Find start of range (01x)
2491 do while (.not.done)
2492 if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2496 phi_start(phi_n) = res_ang(index)
2498 if (index .eq. res_n) done = .true.
2500 ! If a start was found (index < res_n), find the end of range (x10)
2501 ! It may not be found without wrapping around
2502 if (index .lt. res_n) then
2504 do while (.not.done)
2505 if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2510 if (index .eq. res_n) done = .true.
2512 if (index .lt. res_n) then
2513 ! Found the end of the range
2514 phi_end(phi_n) = res_ang(index)
2517 if (index .eq. res_n) then
2523 ! Need to wrap around
2525 phi_end(phi_n) = flag
2529 ! Take care of the last one if need to wrap around
2530 if (phi_end(phi_n) .eq. flag) then
2532 do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2535 phi_end(phi_n) = res_ang(index) + 2.*PI
2541 end subroutine construct_ranges
2542 !-----------------------------------------------------------------------------
2543 subroutine fix_no_moves(phi)
2547 ! include 'COMMON.GEO'
2548 ! include 'COMMON.LOCMOVE'
2555 real(kind=8) :: diff,temp
2558 ! Look for first 01x in gammas (there MUST be at least one)
2561 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2564 if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2565 ! Try to increase PHImax
2566 if (index .gt. 0) then
2567 phi = res_ang(index-1)
2568 diff = abs(res_ang(index) - res_ang(index-1))
2570 ! Look for last (corresponding) x10
2572 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2575 if (index .lt. res_n-1) then
2576 temp = abs(res_ang(index) - res_ang(index+1))
2577 if (temp .lt. diff) then
2578 phi = res_ang(index+1)
2584 ! If increasing PHImax didn't work, decreasing PHImin
2585 ! will (with one exception)
2586 ! Look for first x10 (there MUST be at least one)
2588 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2591 if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2592 ! Try to decrease PHImin
2593 if (index .lt. res_n-1) then
2594 temp = abs(res_ang(index) - res_ang(index+1))
2595 if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2596 phi = res_ang(index+1)
2600 ! Look for last (corresponding) 01x
2602 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2605 if (index .gt. 0) then
2606 temp = abs(res_ang(index) - res_ang(index-1))
2607 if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2608 phi = res_ang(index-1)
2614 ! If it still didn't work, it must be PHImax == 0. or PHImin == PI
2615 if (diff .eq. flag) then
2617 if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2618 res_tab(index,1,2)) index = res_n - 1
2619 ! This MUST work at this point
2620 if (index .eq. 0) then
2623 phi = res_ang(index - 1)
2628 end subroutine fix_no_moves
2629 !-----------------------------------------------------------------------------
2630 integer function move_res(PHImin,PHImax,i_move)
2631 ! Moves residue i_move (in array c), leaving everything else fixed
2632 ! Starting geometry is not checked, it should be correct!
2633 ! R(,i_move) is the only residue that will move, but must have
2634 ! 1 < i_move < nres (i.e., cannot move ends)
2635 ! Whether any output is done is controlled by locmove_output
2637 use random,only:ran_number
2639 ! implicit real*8 (a-h,o-z)
2640 ! include 'DIMENSIONS'
2641 ! include 'COMMON.CHAIN'
2642 ! include 'COMMON.GEO'
2643 ! include 'COMMON.LOCMOVE'
2645 ! External functions
2646 !EL double precision ran_number
2647 !EL external ran_number
2650 real(kind=8) :: PHImin,PHImax
2654 ! 0: move successfull
2655 ! 1: Dmin or Dmax had to be modified
2656 ! 2: move failed - check your input geometry
2660 real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2661 real(kind=8),dimension(0:2) :: P
2662 logical :: no_moves,done
2663 integer :: index,i,j
2664 real(kind=8) :: phi,temp,radius
2665 real(kind=8),dimension(0:11) :: phi_start,phi_end
2668 ! Set up the coordinate system
2670 Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2674 Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2676 temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2682 X(i)=c(i+1,i_move)-Orig(i)
2684 ! radius is the radius of the circle on which c(,i_move) can move
2685 radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2690 Y(0)=Z(1)*X(2)-X(1)*Z(2)
2691 Y(1)=X(0)*Z(2)-Z(0)*X(2)
2692 Y(2)=Z(0)*X(1)-X(0)*Z(1)
2694 ! Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2695 if (i_move.gt.2) then
2697 P(i)=c(i+1,i_move-2)-Orig(i)
2699 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2700 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2701 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2702 radius,a_n,a_ang,a_tab)
2707 ! Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2708 if (i_move.lt.nres-2) then
2710 P(i)=c(i+1,i_move+2)-Orig(i)
2712 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2713 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2714 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2715 radius,b_n,b_ang,b_tab)
2720 ! Construct the resulting table for alpha and beta
2721 call construct_tab()
2723 if (locmove_output) then
2724 print *,'ALPHAS & BETAS TABLE'
2728 ! Check that there is at least one possible move
2730 if (res_n .eq. 0) then
2734 do while ((index .lt. res_n) .and. no_moves)
2735 if (res_tab(2,1,index)) no_moves = .false.
2740 if (locmove_output) print *,' *** Cannot move anywhere'
2745 ! Transfer res_... into a_...
2748 if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2749 (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2750 a_ang(a_n) = res_ang(i)
2752 a_tab(j,a_n) = res_tab(2,j,i)
2758 ! Check that the PHI's are within [0,PI]
2759 if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2760 if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2761 if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2762 if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2763 if (PHImax .lt. PHImin) PHImax = PHImin
2764 ! Calculate min and max angles coming from PHImin and PHImax,
2765 ! and put them in b_...
2766 call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2767 ! Construct the final table
2768 call construct_tab()
2770 if (locmove_output) then
2771 print *,'FINAL TABLE'
2775 ! Check that there is at least one possible move
2777 if (res_n .eq. 0) then
2781 do while ((index .lt. res_n) .and. no_moves)
2782 if (res_tab(2,1,index)) no_moves = .false.
2788 ! Take care of the case where no solution exists...
2789 call fix_no_moves(phi)
2790 if (locmove_output) then
2791 print *,' *** Had to modify PHImin or PHImax'
2792 print *,'phi: ',phi*rad2deg
2796 ! ...or calculate the solution
2797 ! Construct phi_start/phi_end arrays
2798 call construct_ranges(phi_n, phi_start, phi_end)
2799 ! Choose random angle phi in allowed range(s)
2802 temp = temp + phi_end(i) - phi_start(i)
2804 phi = ran_number(phi_start(0),phi_start(0)+temp)
2807 do while (.not.done)
2808 if (phi .lt. phi_end(index)) then
2813 if (index .eq. phi_n) then
2815 else if (.not.done) then
2816 phi = phi + phi_start(index) - phi_end(index-1)
2819 if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2820 if (phi .gt. PI) phi = phi-2.*PI
2822 if (locmove_output) then
2823 print *,'ALLOWED RANGE(S)'
2825 print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2827 print *,'phi: ',phi*rad2deg
2832 ! Re-use radius as temp variable
2833 temp=radius*cos(phi)
2834 radius=radius*sin(phi)
2836 c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2840 end function move_res
2841 !-----------------------------------------------------------------------------
2846 ! implicit real*8 (a-h,o-z)
2847 ! include 'DIMENSIONS'
2848 ! include 'COMMON.GEO'
2849 ! include 'COMMON.LOCAL'
2850 ! include 'COMMON.LOCMOVE'
2852 ! External functions
2853 !EL integer move_res
2854 !EL external move_res
2859 real(kind=8),dimension(0:11) :: phi_start,phi_end
2861 real(kind=8),dimension(0:2,0:5) :: R
2863 locmove_output=.true.
2865 ! call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2866 ! call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2867 ! call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2868 ! call construct_tab
2871 ! call construct_ranges(phi_n,phi_start,phi_end)
2873 ! print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2876 ! call fix_no_moves(phi)
2877 ! print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2883 R(1,1)=-cos(28.D0*deg2rad)
2884 R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2888 R(0,3)=cos(30.D0*deg2rad)
2895 R(1,5)=cos(26.D0*deg2rad)
2896 R(2,5)=0.5D0+sin(26.D0*deg2rad)
2902 ! i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2904 i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2905 print *,'RETURNED ',i
2906 print *,(R(i,3)/vbl,i=0,2)
2909 end subroutine loc_test
2911 !-----------------------------------------------------------------------------
2913 !-----------------------------------------------------------------------------
2914 subroutine MATMULT(A1,A2,A3)
2915 ! implicit real*8 (a-h,o-z)
2916 ! include 'DIMENSIONS'
2919 real(kind=8) :: A3IJ
2921 real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2922 real(kind=8),DIMENSION(3,3) :: AI3
2927 3 A3IJ=A3IJ+A1(I,K)*A2(K,J)
2935 end subroutine MATMULT
2936 !-----------------------------------------------------------------------------
2938 !-----------------------------------------------------------------------------
2939 subroutine int_from_cart(lside,lprn)
2940 ! implicit real*8 (a-h,o-z)
2941 ! include 'DIMENSIONS'
2942 use control_data,only:out1file
2946 ! include 'COMMON.LOCAL'
2947 ! include 'COMMON.VAR'
2948 ! include 'COMMON.CHAIN'
2949 ! include 'COMMON.INTERACT'
2950 ! include 'COMMON.IOUNITS'
2951 ! include 'COMMON.GEO'
2952 ! include 'COMMON.NAMES'
2953 ! include 'COMMON.CONTROL'
2954 ! include 'COMMON.SETUP'
2955 character(len=3) :: seq,res
2957 character(len=80) :: card
2958 real(kind=8),dimension(3,20) :: sccor
2959 integer :: i,j,iti !el rescode,
2960 logical :: lside,lprn
2961 real(kind=8) :: di,cosfac,sinfac
2965 if(me.eq.king.or..not.out1file)then
2967 write (iout,'(/a)') &
2968 'Internal coordinates calculated from crystal structure.'
2970 write (iout,'(8a)') ' Res ',' dvb',' Theta',&
2971 ' Gamma',' Dsc_id',' Dsc',' Alpha',&
2974 write (iout,'(4a)') ' Res ',' dvb',' Theta',&
2980 ! if (molnum(i).ne.1) cycle
2981 !in wham do i=1,nres
2983 if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2984 (iti.ne.ntyp1 .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2985 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2989 vbld(i+1)=dist(i,i+1)
2990 vbld_inv(i+1)=1.0d0/vbld(i+1)
2992 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2993 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2997 ! if (itype(1,1).eq.ntyp1) then
2999 ! c(j,1)=c(j,2)+(c(j,3)-c(j,4))
3002 ! if (itype(nres,1).eq.ntyp1) then
3004 ! c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
3008 ! if (unres_pdb) then
3009 ! if (itype(1,1).eq.21) then
3010 ! theta(3)=90.0d0*deg2rad
3011 ! phi(4)=180.0d0*deg2rad
3013 ! vbld_inv(2)=1.0d0/vbld(2)
3015 ! if (itype(nres,1).eq.21) then
3016 ! theta(nres)=90.0d0*deg2rad
3017 ! phi(nres)=180.0d0*deg2rad
3019 ! vbld_inv(nres)=1.0d0/vbld(2)
3025 c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
3026 +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
3027 ! in wham c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
3032 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3034 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3035 di=dsc(itype(i,molnum(i)))
3037 if (itype(i,1).ne.10) then
3038 vbld_inv(i+nres)=1.0d0/di
3040 vbld_inv(i+nres)=0.0d0
3044 alph(i)=alpha(nres+i,i,nres2+2)
3045 omeg(i)=beta(nres+i,i,nres2+2,i+1)
3048 if(me.eq.king.or..not.out1file)then
3050 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3051 rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3052 rad2deg*alph(i),rad2deg*omeg(i)
3055 if(me.eq.king.or..not.out1file)then
3057 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3058 rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3059 rad2deg*alph(i),rad2deg*omeg(i)
3066 if(me.eq.king.or..not.out1file) &
3067 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3068 rad2deg*theta(i),rad2deg*phi(i)
3072 end subroutine int_from_cart
3073 !-----------------------------------------------------------------------------
3074 subroutine sc_loc_geom(lprn)
3075 ! implicit real*8 (a-h,o-z)
3076 ! include 'DIMENSIONS'
3077 use control_data,only:out1file
3081 ! include 'COMMON.LOCAL'
3082 ! include 'COMMON.VAR'
3083 ! include 'COMMON.CHAIN'
3084 ! include 'COMMON.INTERACT'
3085 ! include 'COMMON.IOUNITS'
3086 ! include 'COMMON.GEO'
3087 ! include 'COMMON.NAMES'
3088 ! include 'COMMON.CONTROL'
3089 ! include 'COMMON.SETUP'
3090 real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3093 integer :: i,j,it,iti
3094 real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3097 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3101 if (itype(i,1).ne.10) then
3103 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3107 dc_norm(j,i+nres)=0.0d0
3112 costtab(i+1) =dcos(theta(i+1))
3113 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3114 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3115 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3116 cosfac2=0.5d0/(1.0d0+costtab(i+1))
3117 cosfac=dsqrt(cosfac2)
3118 sinfac2=0.5d0/(1.0d0-costtab(i+1))
3119 sinfac=dsqrt(sinfac2)
3122 if ((it.ne.10).and.(it.ne.ntyp1)) then
3123 !el if (it.ne.10) then
3125 ! Compute the axes of tghe local cartesian coordinates system; store in
3126 ! x_prime, y_prime and z_prime
3134 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3135 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3137 call vecpr(x_prime,y_prime,z_prime)
3139 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3140 ! to local coordinate system. Store in xx, yy, zz.
3146 xx = xx + x_prime(j)*dc_norm(j,i+nres)
3147 yy = yy + y_prime(j)*dc_norm(j,i+nres)
3148 zz = zz + z_prime(j)*dc_norm(j,i+nres)
3163 if(me.eq.king.or..not.out1file) &
3164 write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3170 end subroutine sc_loc_geom
3171 !-----------------------------------------------------------------------------
3172 subroutine sccenter(ires,nscat,sccor)
3173 ! implicit real*8 (a-h,o-z)
3174 ! include 'DIMENSIONS'
3175 ! include 'COMMON.CHAIN'
3176 integer :: i,j,ires,nscat
3177 real(kind=8),dimension(3,20) :: sccor
3178 real(kind=8) :: sccmj
3179 ! print *,"I am in sccenter",ires,nscat
3183 sccmj=sccmj+sccor(j,i)
3184 !C print *,"insccent", ires,sccor(j,i)
3186 dc(j,ires)=sccmj/nscat
3189 end subroutine sccenter
3190 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3191 !-----------------------------------------------------------------------------
3192 subroutine bond_regular
3194 ! implicit real*8 (a-h,o-z)
3195 ! include 'DIMENSIONS'
3196 ! include 'COMMON.VAR'
3197 ! include 'COMMON.LOCAL'
3198 ! include 'COMMON.CALC'
3199 ! include 'COMMON.INTERACT'
3200 ! include 'COMMON.CHAIN'
3204 vbld_inv(i+1)=1.0d0/vbld(i+1)
3205 vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3206 vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3207 ! print *,vbld(i+1),vbld(i+1+nres)
3210 end subroutine bond_regular
3212 !-----------------------------------------------------------------------------
3214 !-----------------------------------------------------------------------------
3215 subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3216 ! This subroutine calculates unit vectors of a local reference system
3217 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3218 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3219 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3220 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3221 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3222 ! form a linear fragment. Returns vectors e1, e2, and e3.
3223 ! implicit real*8 (a-h,o-z)
3224 ! include 'DIMENSIONS'
3226 real(kind=8),dimension(3) :: e1,e2,e3
3227 real(kind=8),dimension(3) :: u,z
3228 ! include 'COMMON.IOUNITS'
3229 ! include 'COMMON.CHAIN'
3230 real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3232 integer :: i,i1,i2,i3,i4
3233 real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3246 if (s1.gt.coinc) goto 2
3247 write (iout,1000) i2,i3,i1
3252 2 if (s2.gt.coinc) goto 4
3253 write(iout,1000) i3,i4,i1
3260 v1=z(2)*u(3)-z(3)*u(2)
3261 v2=z(3)*u(1)-z(1)*u(3)
3262 v3=z(1)*u(2)-z(2)*u(1)
3263 anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3264 if (anorm.gt.align) goto 6
3265 write (iout,1010) i2,i3,i4,i1
3277 e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3278 e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3279 e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3280 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3281 'coordinates of atom',i4,' are set to zero.')
3282 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3283 ' fragment. coordinates of atom',i4,' are set to zero.')
3285 end subroutine refsys
3286 !-----------------------------------------------------------------------------
3288 !-----------------------------------------------------------------------------
3289 subroutine int_to_cart
3290 !--------------------------------------------------------------
3291 ! This subroutine converts the energy derivatives from internal
3292 ! coordinates to cartesian coordinates
3293 !-------------------------------------------------------------
3294 ! implicit real*8 (a-h,o-z)
3295 ! include 'DIMENSIONS'
3296 ! include 'COMMON.VAR'
3297 ! include 'COMMON.CHAIN'
3298 ! include 'COMMON.DERIV'
3299 ! include 'COMMON.GEO'
3300 ! include 'COMMON.LOCAL'
3301 ! include 'COMMON.INTERACT'
3302 ! include 'COMMON.MD'
3303 ! include 'COMMON.IOUNITS'
3304 ! include 'COMMON.SCCOR'
3305 ! calculating dE/ddc1
3308 ! print *,"gloc",gloc(:,:)
3309 ! print *, "gcart",gcart(:,:)
3310 if (nres.lt.3) go to 18
3312 gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3313 +gloc(nres-2,icg)*dtheta(j,1,3)
3314 if ((itype(2,1).ne.10).and.&
3315 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3316 gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3317 gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3320 ! Calculating the remainder of dE/ddc2
3322 gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3323 gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3324 if(itype(2,1).ne.10) then
3325 gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3326 gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3328 if(itype(3,1).ne.10) then
3329 gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3330 gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3333 gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3336 ! If there are only five residues
3339 gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3340 dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3342 ! if(itype(3,1).ne.10) then
3343 if ((itype(3,1).ne.10).and.&
3344 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3345 gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3346 dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3348 ! if(itype(4,1).ne.10) then
3349 if ((itype(4,1).ne.10).and.&
3350 (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3351 gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3352 dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3356 ! If there are more than five residues
3360 gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3361 +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3362 gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3363 gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3364 if(itype(i,1).ne.10) then
3365 gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3366 gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3368 if(itype(i+1,1).ne.10) then
3369 gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3370 +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3375 ! Setting dE/ddnres-2
3378 gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3379 dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3380 +gloc(2*nres-6,icg)* &
3381 dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3382 if(itype(nres-2,1).ne.10) then
3383 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3384 dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3387 if(itype(nres-1,1).ne.10) then
3388 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3389 dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3394 ! Settind dE/ddnres-1
3398 write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3399 gloc(2*nres-5,icg),dtheta(j,2,nres)
3405 gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3406 gloc(2*nres-5,icg)*dtheta(j,2,nres)
3409 write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3410 gloc(2*nres-5,icg),dtheta(j,2,nres)
3414 if(itype(nres-1,1).ne.10) then
3415 gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3416 dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3420 write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3421 dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3429 ! The side-chain vector derivatives
3431 if(itype(i,1).ne.10 .and. &
3432 itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3434 gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3435 +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3438 write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3439 gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3445 !----------------------------------------------------------------------
3446 ! INTERTYP=1 SC...Ca...Ca...Ca
3447 ! INTERTYP=2 Ca...Ca...Ca...SC
3448 ! INTERTYP=3 SC...Ca...Ca...SC
3449 ! calculating dE/ddc1
3453 ! write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3455 if (nres.lt.2) return
3456 if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3457 if ((itype(1,1).ne.10).and. &
3458 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3460 !c Derviative was calculated for oposite vector of side chain therefore
3461 ! there is "-" sign before gloc_sc
3462 gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3464 gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3466 if ((itype(2,1).ne.10).and. &
3467 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3468 gxcart(j,1)= gxcart(j,1) &
3469 -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3470 gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3475 if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3476 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3479 gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3482 ! As potetnial DO NOT depend on omicron anlge their derivative is
3484 ! & +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3486 ! Calculating the remainder of dE/ddc2
3488 if((itype(2,1).ne.10).and. &
3489 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3490 if ((itype(1,1).ne.10).and.&
3491 ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3492 gxcart(j,2)=gxcart(j,2)+ &
3493 gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3494 if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3496 gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3497 !c the - above is due to different vector direction
3498 gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3501 ! if ((itype(1,1).ne.10).and.&
3502 ! ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3503 gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3504 !c the - above is due to different vector direction
3505 gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3506 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3507 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3510 if ((itype(1,1).ne.10).and.&
3511 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3512 gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3513 ! write(iout,*) gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3515 if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3516 gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3517 ! write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3519 if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3520 gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3521 ! write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3524 ! write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3526 ! If there are more than five residues
3530 ! write(iout,*) "before", gcart(j,i)
3531 if ((itype(i,1).ne.10).and.&
3532 (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3533 gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3534 *dtauangle(j,2,3,i+1) &
3535 -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3536 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3537 *dtauangle(j,1,2,i+2)
3538 ! write(iout,*) "new",j,i,
3539 ! & gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3540 ! if (itype(i-1,1).ne.10) then
3541 if ((itype(i-1,1).ne.10).and.&
3542 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3544 gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3545 *dtauangle(j,3,3,i+1)
3547 ! if (itype(i+1,1).ne.10) then
3548 if ((itype(i+1,1).ne.10).and.&
3549 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3550 gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3551 *dtauangle(j,3,1,i+2)
3552 gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3553 *dtauangle(j,3,2,i+2)
3556 ! if (itype(i-1,1).ne.10) then
3557 if ((itype(i-1,1).ne.10).and.&
3558 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3559 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3560 dtauangle(j,1,3,i+1)
3562 ! if (itype(i+1,1).ne.10) then
3563 if ((itype(i+1,1).ne.10).and.&
3564 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3565 gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3566 dtauangle(j,2,2,i+2)
3567 ! write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3568 ! & dtauangle(j,2,2,i+2)
3570 ! if (itype(i+2,1).ne.10) then
3571 if ((itype(i+2,1).ne.10).and.&
3572 (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3573 gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3574 dtauangle(j,2,1,i+3)
3579 ! Setting dE/ddnres-1
3582 if ((itype(nres-1,1).ne.10).and.&
3583 (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3584 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3585 *dtauangle(j,2,3,nres)
3586 ! write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3587 ! & dtauangle(j,2,3,nres), gxcart(j,nres-1)
3588 ! if (itype(nres-2,1).ne.10) then
3589 if ((itype(nres-2,1).ne.10).and.&
3590 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3591 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3592 *dtauangle(j,3,3,nres)
3594 if ((itype(nres,1).ne.10).and.&
3595 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3596 gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3597 *dtauangle(j,3,1,nres+1)
3598 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3599 *dtauangle(j,3,2,nres+1)
3602 if ((itype(nres-2,1).ne.10).and.&
3603 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3604 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3605 dtauangle(j,1,3,nres)
3607 if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3608 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3609 dtauangle(j,2,2,nres+1)
3610 ! write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3611 ! & dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3616 if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3617 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3619 gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3620 *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3621 *dtauangle(j,2,3,nres+1)
3624 ! The side-chain vector derivatives
3625 ! print *,"gcart",gcart(:,:)
3627 end subroutine int_to_cart
3628 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3629 !-----------------------------------------------------------------------------
3631 !-----------------------------------------------------------------------------
3632 subroutine gen_dist_constr
3633 ! Generate CA distance constraints.
3634 ! implicit real*8 (a-h,o-z)
3635 ! include 'DIMENSIONS'
3636 ! include 'COMMON.IOUNITS'
3637 ! include 'COMMON.GEO'
3638 ! include 'COMMON.VAR'
3639 ! include 'COMMON.INTERACT'
3640 ! include 'COMMON.LOCAL'
3641 ! include 'COMMON.NAMES'
3642 ! include 'COMMON.CHAIN'
3643 ! include 'COMMON.FFIELD'
3644 ! include 'COMMON.SBRIDGE'
3645 ! include 'COMMON.HEADER'
3646 ! include 'COMMON.CONTROL'
3647 ! include 'COMMON.DBASE'
3648 ! include 'COMMON.THREAD'
3649 ! include 'COMMON.TIME1'
3650 ! integer :: itype_pdb !(maxres)
3651 ! common /pizda/ itype_pdb(nres)
3652 character(len=2) :: iden
3655 !d print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3656 !d write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3657 !d & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3659 do i=nstart_sup,nstart_sup+nsup-1
3660 !d write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3661 !d & ' seq_pdb', restyp(itype_pdb(i))
3662 do j=i+2,nstart_sup+nsup-1
3664 ihpb(nhpb)=i+nstart_seq-nstart_sup
3665 jhpb(nhpb)=j+nstart_seq-nstart_sup
3667 dhpb(nhpb)=dist(i,j)
3670 !d write (iout,'(a)') 'Distance constraints:'
3675 !d if (ii.gt.nres) then
3680 !d write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3681 !d & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3682 !d & dhpb(i),forcon(i)
3684 ! deallocate(itype_pdb)
3687 end subroutine gen_dist_constr
3689 !-----------------------------------------------------------------------------
3691 !-----------------------------------------------------------------------------
3692 subroutine cartprint
3694 use geometry_data, only: c
3695 use energy_data, only: itype
3696 ! implicit real*8 (a-h,o-z)
3697 ! include 'DIMENSIONS'
3698 ! include 'COMMON.CHAIN'
3699 ! include 'COMMON.INTERACT'
3700 ! include 'COMMON.NAMES'
3701 ! include 'COMMON.IOUNITS'
3706 write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3707 c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3709 100 format (//' alpha-carbon coordinates ',&
3710 ' centroid coordinates'/ &
3711 ' ', 6X,'X',11X,'Y',11X,'Z',&
3712 10X,'X',11X,'Y',11X,'Z')
3713 110 format (a,'(',i3,')',6f12.5)
3715 end subroutine cartprint
3716 !-----------------------------------------------------------------------------
3717 !-----------------------------------------------------------------------------
3718 subroutine alloc_geo_arrays
3719 !EL Allocation of tables used by module energy
3721 integer :: i,j,nres2
3725 allocate(phibound(2,nres+2)) !(2,maxres)
3726 !----------------------
3728 ! common /chain/ in molread
3729 ! real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3730 ! real(kind=8),dimension(:,:),allocatable :: dc
3731 allocate(dc_old(3,0:nres2))
3732 ! if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3733 if(.not.allocated(dc_norm2)) then
3734 allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3738 !el if(.not.allocated(dc_norm))
3739 !elwrite(iout,*) "jestem w alloc geo 1"
3740 if(.not.allocated(dc_norm)) then
3741 allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3744 !elwrite(iout,*) "jestem w alloc geo 1"
3745 allocate(xloc(3,nres),xrot(3,nres))
3746 !elwrite(iout,*) "jestem w alloc geo 1"
3748 !elwrite(iout,*) "jestem w alloc geo 1"
3749 allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3751 allocate(t(3,3,nres),r(3,3,nres))
3752 allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3753 ! common /refstruct/
3754 if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3755 !elwrite(iout,*) "jestem w alloc geo 2"
3756 allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3757 if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3758 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3759 ! common /from_zscore/ in module.compare
3760 !----------------------
3762 ! Inverses of the actual virtual bond lengths
3763 ! common /invlen/ in io_conf: molread or readpdb
3764 ! real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3765 !----------------------
3767 ! Store the geometric variables in the following COMMON block.
3768 ! common /var/ in readpdb or ...
3769 if(.not.allocated(theta)) allocate(theta(nres+2))
3770 if(.not.allocated(phi)) allocate(phi(nres+2))
3771 if(.not.allocated(alph)) allocate(alph(nres+2))
3772 if(.not.allocated(omeg)) allocate(omeg(nres+2))
3773 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3774 if(.not.allocated(phiref)) allocate(phiref(nres+2))
3775 if(.not.allocated(costtab)) allocate(costtab(nres))
3776 if(.not.allocated(sinttab)) allocate(sinttab(nres))
3777 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3778 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3779 ! real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3780 allocate(omicron(2,nres+2)) !(2,maxres)
3781 allocate(tauangle(3,nres+2)) !(3,maxres)
3782 !elwrite(iout,*) "jestem w alloc geo 3"
3783 if(.not.allocated(xxtab)) allocate(xxtab(nres))
3784 if(.not.allocated(yytab)) allocate(yytab(nres))
3785 if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3786 if(.not.allocated(xxref)) allocate(xxref(nres))
3787 if(.not.allocated(yyref)) allocate(yyref(nres))
3788 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3789 allocate(ialph(nres,2)) !(maxres,2)
3792 allocate(ivar(4*nres2)) !(4*maxres2)
3794 #if defined(WHAM_RUN) || defined(CLUSTER)
3795 allocate(vbld(2*nres))
3797 allocate(vbld_inv(2*nres))
3802 end subroutine alloc_geo_arrays
3803 !-----------------------------------------------------------------------------
3804 !-----------------------------------------------------------------------------
3805 subroutine returnbox
3806 integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3807 integer :: chain_end,ireturnval
3808 real*8 :: difference
3809 !C change suggested by Ana - end
3813 !C write(*,*) 'initial', i,j,c(j,i)
3815 !C change suggested by Ana - begin
3817 !C change suggested by Ana -end
3820 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3821 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3823 if (allareout.eq.1) then
3824 ireturnval=int(c(j,i)/boxxsize)
3825 if (c(j,i).le.0) ireturnval=ireturnval-1
3826 do k=chain_beg,chain_end
3827 c(j,k)=c(j,k)-ireturnval*boxxsize
3828 c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3831 if (chain_beg.eq.1) &
3832 dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3833 !C Suggested by Ana -end
3838 if (int(c(j,i)/boxxsize).eq.0) allareout=0
3841 if (allareout.eq.1) then
3842 ireturnval=int(c(j,i)/boxxsize)
3843 if (c(j,i).le.0) ireturnval=ireturnval-1
3845 c(j,k)=c(j,k)-ireturnval*boxxsize
3846 c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3851 !C write(*,*) 'befor no jump', i,j,c(j,i)
3856 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3857 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3858 difference=abs(c(j,i-1)-c(j,i))
3859 !C print *,'diff', difference
3860 if (difference.gt.boxxsize/2.0) then
3861 if (c(j,i-1).gt.c(j,i)) then
3870 c(j,i)=c(j,i)+nojumpval*boxxsize
3871 c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3876 if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3877 difference=abs(c(j,i-1)-c(j,i))
3878 if (difference.gt.boxxsize/2.0) then
3879 if (c(j,i-1).gt.c(j,i)) then
3888 c(j,i)=c(j,i)+nojumpval*boxxsize
3889 c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3893 !C write(*,*) 'after no jump', i,j,c(j,i)
3897 !C suggesed by Ana begins
3903 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3904 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3906 if (allareout.eq.1) then
3907 ireturnval=int(c(j,i)/boxysize)
3908 if (c(j,i).le.0) ireturnval=ireturnval-1
3909 do k=chain_beg,chain_end
3910 c(j,k)=c(j,k)-ireturnval*boxysize
3911 c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3914 if (chain_beg.eq.1) &
3915 dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3916 !C Suggested by Ana -end
3921 if (int(c(j,i)/boxysize).eq.0) allareout=0
3924 if (allareout.eq.1) then
3925 ireturnval=int(c(j,i)/boxysize)
3926 if (c(j,i).le.0) ireturnval=ireturnval-1
3928 c(j,k)=c(j,k)-ireturnval*boxysize
3929 c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3935 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3936 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3937 difference=abs(c(j,i-1)-c(j,i))
3938 if (difference.gt.boxysize/2.0) then
3939 if (c(j,i-1).gt.c(j,i)) then
3948 c(j,i)=c(j,i)+nojumpval*boxysize
3949 c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3954 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3955 .and. itype(i-1,mnum).eq.ntyp1) then
3956 difference=abs(c(j,i-1)-c(j,i))
3957 if (difference.gt.boxysize/2.0) then
3958 if (c(j,i-1).gt.c(j,i)) then
3967 c(j,i)=c(j,i)+nojumpval*boxysize
3968 c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3971 !C Suggested by Ana -begins
3973 !C Suggested by Ana -ends
3978 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3979 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3981 if (allareout.eq.1) then
3982 ireturnval=int(c(j,i)/boxysize)
3983 if (c(j,i).le.0) ireturnval=ireturnval-1
3984 do k=chain_beg,chain_end
3985 c(j,k)=c(j,k)-ireturnval*boxzsize
3986 c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3989 if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3990 !C Suggested by Ana -end
3995 if (int(c(j,i)/boxzsize).eq.0) allareout=0
3998 if (allareout.eq.1) then
3999 ireturnval=int(c(j,i)/boxzsize)
4000 if (c(j,i).le.0) ireturnval=ireturnval-1
4002 c(j,k)=c(j,k)-ireturnval*boxzsize
4003 c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
4009 if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4010 difference=abs(c(j,i-1)-c(j,i))
4011 if (difference.gt.(boxzsize/2.0)) then
4012 if (c(j,i-1).gt.c(j,i)) then
4021 c(j,i)=c(j,i)+nojumpval*boxzsize
4022 c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4027 if (itype(i,mnum).eq.ntyp1_molec(mnum) &
4028 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4029 difference=abs(c(j,i-1)-c(j,i))
4030 if (difference.gt.boxzsize/2.0) then
4031 if (c(j,i-1).gt.c(j,i)) then
4040 c(j,i)=c(j,i)+nojumpval*boxzsize
4041 c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4044 if (molnum(i).eq.5) then
4045 c(1,i)=dmod(c(1,i),boxxsize)
4046 c(2,i)=dmod(c(2,i),boxysize)
4047 c(3,i)=dmod(c(3,i),boxzsize)
4048 c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4049 c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4050 c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4054 end subroutine returnbox
4055 !-------------------------------------------------------------------------------------------------------