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
861 do while (i.le.nres .and. niter.lt.maxgen)
862 write(iout,*) 'i=',i,'back=',back
863 if (i.lt.nstart) then
865 write (iout,'(/80(1h*)/2a/80(1h*))') &
866 'Generation procedure went down to ',&
867 'chain beginning. Cannot continue...'
868 write (*,'(/80(1h*)/2a/80(1h*))') &
869 'Generation procedure went down to ',&
870 'chain beginning. Cannot continue...'
874 it1=iabs(itype(i-1,molnum(i-1)))
875 it2=iabs(itype(i-2,molnum(i-2)))
876 it=iabs(itype(i,molnum(i)))
877 if ((it.eq.ntyp1).and.(it1.eq.ntyp1)) &
878 vbld(i)=ran_number(30.0D0,40.0D0)
879 ! print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,&
880 ! ' nit=',nit,' niter=',niter,' maxgen=',maxgen
881 phi(i+1)=gen_phi(i+1,it1,it)
883 phi(i)=gen_phi(i+1,it2,it1)
884 ! print *,'phi(',i,')=',phi(i)
885 theta(i-1)=gen_theta(it2,phi(i-1),phi(i),molnum(i))
886 ! print *,"theta",theta(i-1),phi(i)
887 if ((it2.ne.10).and.(it2.ne.ntyp1)) then
890 do while (fail.and.nsi.le.maxsi)
891 call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail,molnum(i-2))
894 if (nsi.gt.maxsi) return 1
896 call locate_next_res(i-1)
898 theta(i)=gen_theta(it1,phi(i),phi(i+1),molnum(i))
899 ! write(iout,*) "theta(i),",theta(i)
900 if ((it1.ne.10).and.(it1.ne.ntyp1)) then
903 do while (fail.and.nsi.le.maxsi)
904 call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail,molnum(i))
905 ! write(iout,*)"alpha,omeg(i-1)",alph(i-1),omeg(i-1),i,nsi,maxsi
908 if (nsi.gt.maxsi) return 1
910 call locate_next_res(i)
911 write(iout,*) "overlap,",overlap(i-1)
912 if (overlap(i-1)) then
913 if (nit.lt.maxnit) then
923 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
925 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
930 ! write(iout,*) "tu dochodze"
937 if (niter.ge.maxgen) then
938 write (iout,'(a,2i5)') &
939 'Too many trials in conformation generation',niter,maxgen
940 write (*,'(a,2i5)') &
941 'Too many trials in conformation generation',niter,maxgen
946 c(j,nres+nres)=c(j,nres)
949 end subroutine gen_rand_conf
950 !-----------------------------------------------------------------------------
951 logical function overlap(i)
952 ! implicit real*8 (a-h,o-z)
953 ! include 'DIMENSIONS'
954 ! include 'COMMON.CHAIN'
955 ! include 'COMMON.INTERACT'
956 ! include 'COMMON.FFIELD'
957 integer :: i,j,iti,itj,iteli,itelj,k
958 real(kind=8) :: redfac,rcomp
963 iti=iabs(itype(i,molnum(i)))
964 if (iti.gt.ntyp) return
965 ! Check for SC-SC overlaps.
966 !d print *,'nnt=',nnt,' nct=',nct
968 ! print *, "molnum(j)",j,molnum(j)
969 if (molnum(j).eq.1) then
971 if (itj.eq.ntyp1) cycle
972 if (j.lt.i-1 .or. ipot.ne.4) then
973 rcomp=sigmaii(iti,itj)
978 if (dist(nres+i,nres+j).lt.redfac*rcomp) then
981 ! print *,'overlap, SC-SC: i=',i,' j=',j,
982 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
986 else if (molnum(j).eq.2) then
988 if (dist(nres+i,nres+j).lt.redfac*sigma_nucl(iti,itj)) then
991 ! print *,'overlap, SC-SC: i=',i,' j=',j,
992 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
999 ! Check for overlaps between the added peptide group and the preceding
1003 ! c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
1004 c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1007 if (molnum(j).ne.1) cycle
1008 itj=iabs(itype(j,1))
1009 !d print *,'overlap, p-Sc: i=',i,' j=',j,
1010 !d & ' dist=',dist(nres+j,maxres2+1)
1011 if (dist(nres+j,nres2+3).lt.4.0D0*redfac) then
1016 ! Check for overlaps between the added side chain and the preceding peptide
1019 if (molnum(j).ne.1) cycle
1021 c(k,nres2+3)=0.5D0*(c(k,j)+c(k,j+1))
1023 !d print *,'overlap, SC-p: i=',i,' j=',j,
1024 !d & ' dist=',dist(nres+i,maxres2+1)
1025 if (dist(nres+i,nres2+3).lt.4.0D0*redfac) then
1030 ! Check for p-p overlaps
1032 c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1035 ! if (molnum(j).eq.1) then
1038 c(k,nres2+4)=0.5D0*(c(k,j)+c(k,j+1))
1040 !d print *,'overlap, p-p: i=',i,' j=',j,
1041 !d & ' dist=',dist(maxres2+1,maxres2+2)
1042 if (molnum(j).eq.1) then
1043 if(iteli.ne.0.and.itelj.ne.0)then
1044 if (dist(nres2+3,nres2+4).lt.rpp(iteli,itelj)*redfac) then
1049 else if (molnum(j).eq.2) then
1050 if (dist(nres2+3,nres2+4).lt.3.0) then
1057 end function overlap
1058 !-----------------------------------------------------------------------------
1059 real(kind=8) function gen_phi(i,it1,it2)
1060 use random, only:ran_number
1061 ! implicit real*8 (a-h,o-z)
1062 ! include 'DIMENSIONS'
1063 ! include 'COMMON.GEO'
1064 ! include 'COMMON.BOUNDS'
1065 integer :: i,it1,it2
1066 ! gen_phi=ran_number(-pi,pi)
1067 ! 8/13/98 Generate phi using pre-defined boundaries
1068 gen_phi=ran_number(phibound(1,i),phibound(2,i))
1070 end function gen_phi
1071 !-----------------------------------------------------------------------------
1072 real(kind=8) function gen_theta(it,gama,gama1,mnum)
1073 use random,only:binorm,ran_number
1074 ! implicit real*8 (a-h,o-z)
1075 ! include 'DIMENSIONS'
1076 ! include 'COMMON.LOCAL'
1077 ! include 'COMMON.GEO'
1078 real(kind=8),dimension(2) :: y,z
1079 real(kind=8) :: theta_max,theta_min,sig,ak
1081 integer :: j,it,k,mnum
1082 real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1083 ! print *,'gen_theta: it=',it
1086 if (dabs(gama).gt.dwapi) then
1093 if (dabs(gama1).gt.dwapi) then
1100 if (it.eq.ntyp1) then
1101 gen_theta=ran_number(theta_max/2.0,theta_max)
1102 else if (mnum.eq.1) then
1104 thet_pred_mean=a0thet(it)
1105 ! write(iout,*),it,thet_pred_mean,"gen_thet"
1107 thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1108 +bthet(k,it,1,1)*z(k)
1112 sig=sig*thet_pred_mean+polthet(j,it)
1114 sig=0.5D0/(sig*sig+sigc0(it))
1115 ak=dexp(gthet(1,it)- &
1116 0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1117 ! print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1118 ! print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1119 theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1120 if (theta_temp.lt.theta_min) theta_temp=theta_min
1121 if (theta_temp.gt.theta_max) theta_temp=theta_max
1122 gen_theta=theta_temp
1123 ! print '(a)','Exiting GENTHETA.'
1124 else if (mnum.eq.2) then
1125 gen_theta=2.0d0 + ran_number(0.0d0,0.34d0)
1127 gen_theta=ran_number(theta_max/2.0,theta_max)
1130 end function gen_theta
1131 !-----------------------------------------------------------------------------
1132 subroutine gen_side(it,the,al,om,fail,mnum)
1133 use random, only:ran_number,mult_norm1
1134 ! implicit real*8 (a-h,o-z)
1135 ! include 'DIMENSIONS'
1136 ! include 'COMMON.GEO'
1137 ! include 'COMMON.LOCAL'
1138 ! include 'COMMON.SETUP'
1139 ! include 'COMMON.IOUNITS'
1140 real(kind=8) :: MaxBoxLen=10.0D0
1141 real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1142 real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1143 real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1144 real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1145 real(kind=8),dimension(2) :: y,cm,eig
1146 real(kind=8),dimension(2,2) :: box
1147 real(kind=8),dimension(100) :: work
1148 real(kind=8) :: eig_limit=1.0D-8
1149 real(kind=8) :: Big=10.0D0
1150 logical :: lprint,fail,lcheck
1152 integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob,mnum
1153 real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1154 real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1155 real(kind=8) :: which_lobe
1160 if (the.eq.0.0D0 .or. the.eq.pi) then
1162 write (*,'(a,i4,a,i3,a,1pe14.5)') &
1163 'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1165 !d write (iout,'(a,i3,a,1pe14.5)')
1166 !d & 'Error in GenSide: it=',it,' theta=',the
1171 if (nlobit.eq.0) then
1172 al=ran_number(0.05d0,pi/6)
1173 om=ran_number(-pi,pi)
1176 tant=dtan(the-pipol)
1178 allocate(z(3,nlobit))
1179 allocate(W1(nlobit))
1180 allocate(detAp(nlobit))
1181 allocate(sumW(0:nlobit))
1184 print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1185 write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1187 print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1188 write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1192 zz1=tant-censc(1,i,it)
1195 a(k,l)=gaussc(k,l,i,it)
1198 detApi=a(2,2)*a(3,3)-a(2,3)**2
1199 Ap_inv(2,2)=a(3,3)/detApi
1200 Ap_inv(2,3)=-a(2,3)/detApi
1201 Ap_inv(3,2)=Ap_inv(2,3)
1202 Ap_inv(3,3)=a(2,2)/detApi
1204 write (*,'(/a,i2/)') 'Cluster #',i
1205 write (*,'(3(1pe14.5),5x,1pe14.5)') &
1206 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1207 write (iout,'(/a,i2/)') 'Cluster #',i
1208 write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1209 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1214 W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1218 W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1219 ! if (lprint) write(*,'(a,3(1pe15.5)/)')
1220 ! & 'detAp, W1, anormi',detApi,W1i,anormi
1224 zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1228 detAp(i)=dsqrt(detApi)
1232 print *,'W1:',(w1(i),i=1,nlobit)
1233 print *,'detAp:',(detAp(i),i=1,nlobit)
1236 print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1238 write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1239 write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1242 write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1246 ! Writing the distribution just to check the procedure
1248 dV=deg2rad**2*10.0D0
1252 fac=fac+W1(i)/detAp(i)
1254 fac=1.0D0/(2.0D0*fac*pi)
1255 !d print *,it,'fac=',fac
1264 a(j-1,k-1)=gaussc(j,k,i,it)
1276 wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1279 wart=wart+W1(i)*dexp(-0.5D0*wykl)
1286 ! print *,'y',y(1),y(2),' fac=',fac
1288 write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1293 ! print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1297 ! Calculate the CM of the system
1300 W1(i)=W1(i)/detAp(i)
1304 sumW(i)=sumW(i-1)+W1(i)
1309 cm(1)=cm(1)+z(2,j)*W1(j)
1310 cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1312 cm(1)=cm(1)/sumW(nlobit)
1313 cm(2)=cm(2)/sumW(nlobit)
1314 if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1315 cm(2).gt.Big .or. cm(2).lt.-Big) then
1316 !d write (iout,'(a)')
1317 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1318 !d write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1320 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1321 !d write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1325 !d print *,'CM:',cm(1),cm(2)
1327 ! Find the largest search distance from CM
1333 a(j-1,k-1)=gaussc(j,k,i,it)
1337 call f02faf('N','U',2,a,3,eig,work,100,ifail)
1339 call djacob(2,3,10000,1.0d-10,a,vec,eig)
1343 print *,'*************** CG Processor',me
1344 print *,'CM:',cm(1),cm(2)
1345 write (iout,*) '*************** CG Processor',me
1346 write (iout,*) 'CM:',cm(1),cm(2)
1347 print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1348 write (iout,'(A,8f10.5)') &
1349 'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1352 if (eig(1).lt.eig_limit) then
1354 'From Mult_Norm: Eigenvalues of A are too small.'
1356 'From Mult_Norm: Eigenvalues of A are too small.'
1363 radius=radius+pinorm(z(j+1,i)-cm(j))**2
1365 radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1366 if (radius.gt.radmax) radmax=radius
1368 if (radmax.gt.pi) radmax=pi
1370 ! Determine the boundaries of the search rectangle.
1373 print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1374 print '(a,4(1pe14.4))','radmax: ',radmax
1376 box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1377 box(2,1)=dmin1(cm(1)+radmax,pi)
1378 box(1,2)=cm(2)-radmax
1379 box(2,2)=cm(2)+radmax
1382 print *,'CG Processor',me,' Array BOX:'
1384 print *,'Array BOX:'
1386 print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1387 print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1389 write (iout,*)'CG Processor',me,' Array BOX:'
1391 write (iout,*)'Array BOX:'
1393 write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1394 write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1396 ! if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1398 ! write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1399 ! write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1401 ! write (iout,'(a)') 'Bad sampling box.'
1406 which_lobe=ran_number(0.0D0,sumW(nlobit))
1407 ! print '(a,1pe14.4)','which_lobe=',which_lobe
1409 if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1412 ! print *,'ilob=',ilob,' nlob=',nlob(it)
1416 a(i-1,j-1)=gaussc(i,j,ilob,it)
1419 !d print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1420 call mult_norm1(3,2,a,cm,box,y,fail)
1424 else if (mnum.eq.2) then
1425 al=0.7+ran_number(0.0d0,0.2d0)
1426 om=ran_number(0.0d0,3.14d0)
1429 !d print *,'al=',al,' om=',om
1432 end subroutine gen_side
1433 !-----------------------------------------------------------------------------
1434 subroutine overlap_sc(scfail)
1436 ! Internal and cartesian coordinates must be consistent as input,
1437 ! and will be up-to-date on return.
1438 ! At the end of this procedure, scfail is true if there are
1439 ! overlapping residues left, or false otherwise (success)
1441 ! implicit real*8 (a-h,o-z)
1442 ! include 'DIMENSIONS'
1443 ! include 'COMMON.CHAIN'
1444 ! include 'COMMON.INTERACT'
1445 ! include 'COMMON.FFIELD'
1446 ! include 'COMMON.VAR'
1447 ! include 'COMMON.SBRIDGE'
1448 ! include 'COMMON.IOUNITS'
1449 logical :: had_overlaps,fail,scfail
1450 integer,dimension(nres) :: ioverlap !(maxres)
1451 integer :: ioverlap_last,k,maxsi,i,iti,nsi
1454 had_overlaps=.false.
1455 call overlap_sc_list(ioverlap,ioverlap_last)
1456 if (ioverlap_last.gt.0) then
1457 write (iout,*) '#OVERLAPing residues ',ioverlap_last
1458 write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1464 if (ioverlap_last.eq.0) exit
1466 do ires=1,ioverlap_last
1468 iti=iabs(itype(i,1))
1469 if ((iti.ne.10).and.(molnum(i).ne.5).and.(iti.ne.ntyp1)) then
1472 do while (fail.and.nsi.le.maxsi)
1473 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1481 call overlap_sc_list(ioverlap,ioverlap_last)
1482 ! write (iout,*) 'Overlaping residues ',ioverlap_last,
1483 ! & (ioverlap(j),j=1,ioverlap_last)
1486 if (k.le.1000.and.ioverlap_last.eq.0) then
1488 if (had_overlaps) then
1489 write (iout,*) '#OVERLAPing all corrected after ',k,&
1490 ' random generation'
1494 write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1495 write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1501 write (iout,'(a30,i5,a12,i4)') &
1502 '#OVERLAP FAIL in gen_side after',maxsi,&
1506 end subroutine overlap_sc
1507 !-----------------------------------------------------------------------------
1508 subroutine overlap_sc_list(ioverlap,ioverlap_last)
1510 ! implicit real*8 (a-h,o-z)
1511 ! include 'DIMENSIONS'
1512 ! include 'COMMON.GEO'
1513 ! include 'COMMON.LOCAL'
1514 ! include 'COMMON.IOUNITS'
1515 ! include 'COMMON.CHAIN'
1516 ! include 'COMMON.INTERACT'
1517 ! include 'COMMON.FFIELD'
1518 ! include 'COMMON.VAR'
1519 ! include 'COMMON.CALC'
1521 integer,dimension(nres) :: ioverlap !(maxres)
1522 integer :: ioverlap_last
1525 real(kind=8) :: redfac,sig !rrij,sigsq,
1526 integer :: itypi,itypj,itypi1
1527 real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1531 ! Check for SC-SC overlaps and mark residues
1532 ! print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1534 do i=iatsc_s,iatsc_e
1535 if (itype(i,molnum(i)).eq.ntyp1_molec(molnum(i))) cycle
1536 if (molnum(i).eq.5) print *,"WTF",i,iatsc_s,iatsc_e
1537 if (molnum(i).eq.5) cycle
1538 itypi=iabs(itype(i,molnum(i)))
1539 itypi1=iabs(itype(i+1,1))
1543 dxi=dc_norm(1,nres+i)
1544 dyi=dc_norm(2,nres+i)
1545 dzi=dc_norm(3,nres+i)
1546 dsci_inv=dsc_inv(itypi)
1548 do iint=1,nint_gr(i)
1549 do j=istart(i,iint),iend(i,iint)
1550 if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
1552 itypj=iabs(itype(j,molnum(j)))
1553 dscj_inv=dsc_inv(itypj)
1554 sig0ij=sigma(itypi,itypj)
1555 chi1=chi(itypi,itypj)
1556 chi2=chi(itypj,itypi)
1563 alf12=0.5D0*(alf1+alf2)
1565 rcomp=sigmaii(itypi,itypj)
1567 rcomp=sigma(itypi,itypj)
1569 ! print '(2(a3,2i3),a3,2f10.5)',
1570 ! & ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1575 dxj=dc_norm(1,nres+j)
1576 dyj=dc_norm(2,nres+j)
1577 dzj=dc_norm(3,nres+j)
1578 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1582 sig=sig0ij*dsqrt(sigsq)
1583 rij_shift=1.0D0/rij-sig+sig0ij
1585 !t if ( 1.0/rij .lt. redfac*rcomp .or.
1586 !t & rij_shift.le.0.0D0 ) then
1587 if ( rij_shift.le.0.0D0 ) then
1588 !d write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1589 !d & 'overlap SC-SC: i=',i,' j=',j,
1590 !d & ' dist=',dist(nres+i,nres+j),' rcomp=',
1591 !d & rcomp,1.0/rij,rij_shift
1592 ioverlap_last=ioverlap_last+1
1593 ioverlap(ioverlap_last)=i
1594 do k=1,ioverlap_last-1
1595 if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1597 ioverlap_last=ioverlap_last+1
1598 ioverlap(ioverlap_last)=j
1599 do k=1,ioverlap_last-1
1600 if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1607 end subroutine overlap_sc_list
1609 !-----------------------------------------------------------------------------
1610 ! energy_p_new_barrier.F
1611 !-----------------------------------------------------------------------------
1612 subroutine sc_angular
1613 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1614 ! om12. Called by ebp, egb, and egbv.
1617 ! include 'COMMON.CALC'
1618 ! include 'COMMON.IOUNITS'
1622 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1623 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1624 om12=dxi*dxj+dyi*dyj+dzi*dzj
1626 ! Calculate eps1(om12) and its derivative in om12
1627 faceps1=1.0D0-om12*chiom12
1628 faceps1_inv=1.0D0/faceps1
1629 eps1=dsqrt(faceps1_inv)
1630 ! Following variable is eps1*deps1/dom12
1631 eps1_om12=faceps1_inv*chiom12
1636 ! write (iout,*) "om12",om12," eps1",eps1
1637 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1642 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1643 sigsq=1.0D0-facsig*faceps1_inv
1644 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1645 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1646 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1652 ! write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1653 ! write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1655 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1658 chipom12=chip12*om12
1659 facp=1.0D0-om12*chipom12
1661 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1662 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1663 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1664 ! Following variable is the square root of eps2
1665 eps2rt=1.0D0-facp1*facp_inv
1666 ! Following three variables are the derivatives of the square root of eps
1667 ! in om1, om2, and om12.
1668 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1669 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1670 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1671 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1672 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1673 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1674 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1675 ! & " eps2rt_om12",eps2rt_om12
1676 ! Calculate whole angle-dependent part of epsilon and contributions
1677 ! to its derivatives
1679 end subroutine sc_angular
1680 !-----------------------------------------------------------------------------
1682 subroutine sc_angular_nucl
1683 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1684 ! om12. Called by ebp, egb, and egbv.
1687 ! include 'COMMON.CALC'
1688 ! include 'COMMON.IOUNITS'
1694 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1695 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1696 om12=dxi*dxj+dyi*dyj+dzi*dzj
1698 ! Calculate eps1(om12) and its derivative in om12
1699 faceps1=1.0D0-om12*chiom12
1700 faceps1_inv=1.0D0/faceps1
1701 eps1=dsqrt(faceps1_inv)
1702 ! Following variable is eps1*deps1/dom12
1703 eps1_om12=faceps1_inv*chiom12
1708 ! write (iout,*) "om12",om12," eps1",eps1
1709 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1714 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1715 sigsq=1.0D0-facsig*faceps1_inv
1716 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1717 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1718 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1721 chipom12=chip12*om12
1722 facp=1.0D0-om12*chipom12
1724 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1725 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1726 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1727 ! Following variable is the square root of eps2
1728 eps2rt=1.0D0-facp1*facp_inv
1729 ! Following three variables are the derivatives of the square root of eps
1730 ! in om1, om2, and om12.
1731 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1732 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1733 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1734 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1735 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1736 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1737 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1738 ! & " eps2rt_om12",eps2rt_om12
1739 ! Calculate whole angle-dependent part of epsilon and contributions
1740 ! to its derivatives
1742 end subroutine sc_angular_nucl
1744 !-----------------------------------------------------------------------------
1745 subroutine int_bounds(total_ints,lower_bound,upper_bound)
1746 ! implicit real*8 (a-h,o-z)
1747 ! include 'DIMENSIONS'
1749 ! include 'COMMON.SETUP'
1750 integer :: total_ints,lower_bound,upper_bound,nint
1751 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1752 integer :: i,nexcess
1753 nint=total_ints/nfgtasks
1757 nexcess=total_ints-nint*nfgtasks
1759 int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1763 lower_bound=lower_bound+int4proc(i)
1765 upper_bound=lower_bound+int4proc(fg_rank)
1766 lower_bound=lower_bound+1
1768 end subroutine int_bounds
1769 !-----------------------------------------------------------------------------
1770 subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1771 ! implicit real*8 (a-h,o-z)
1772 ! include 'DIMENSIONS'
1774 ! include 'COMMON.SETUP'
1775 integer :: total_ints,lower_bound,upper_bound,nint
1776 integer :: nexcess,i
1777 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1778 nint=total_ints/nfgtasks1
1782 nexcess=total_ints-nint*nfgtasks1
1784 int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1788 lower_bound=lower_bound+int4proc(i)
1790 upper_bound=lower_bound+int4proc(fg_rank1)
1791 lower_bound=lower_bound+1
1793 end subroutine int_bounds1
1794 !-----------------------------------------------------------------------------
1796 !-----------------------------------------------------------------------------
1797 subroutine chainbuild_cart
1798 ! implicit real*8 (a-h,o-z)
1799 ! include 'DIMENSIONS'
1804 ! include 'COMMON.SETUP'
1805 ! include 'COMMON.CHAIN'
1806 ! include 'COMMON.LOCAL'
1807 ! include 'COMMON.TIME1'
1808 ! include 'COMMON.IOUNITS'
1809 integer :: j,i,ierror,ierr
1810 real(kind=8) :: time00,time01
1812 if (nfgtasks.gt.1) then
1813 ! write (iout,*) "BCAST in chainbuild_cart"
1815 ! Broadcast the order to build the chain and compute internal coordinates
1816 ! to the slaves. The slaves receive the order in ERGASTULUM.
1818 ! write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1820 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1821 ! & (dc(j,i+nres),j=1,3)
1824 call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1825 time_bcast7=time_bcast7+MPI_Wtime()-time00
1827 call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1829 ! write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1831 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1832 ! & (dc(j,i+nres),j=1,3)
1834 ! write (iout,*) "End BCAST in chainbuild_cart"
1836 time_bcast=time_bcast+MPI_Wtime()-time00
1837 time_bcastc=time_bcastc+MPI_Wtime()-time01
1845 c(j,i)=c(j,i-1)+dc(j,i-1)
1850 c(j,i+nres)=c(j,i)+dc(j,i+nres)
1853 ! write (iout,*) "CHAINBUILD_CART"
1855 call int_from_cart1(.false.)
1857 end subroutine chainbuild_cart
1858 !-----------------------------------------------------------------------------
1860 !-----------------------------------------------------------------------------
1861 real(kind=8) function alpha(i1,i2,i3)
1863 ! Calculates the planar angle between atoms (i1), (i2), and (i3).
1865 ! implicit real*8 (a-h,o-z)
1866 ! include 'DIMENSIONS'
1867 ! include 'COMMON.GEO'
1868 ! include 'COMMON.CHAIN'
1871 real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1878 vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1879 wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1880 scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1884 !-----------------------------------------------------------------------------
1885 real(kind=8) function beta(i1,i2,i3,i4)
1887 ! Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1889 ! implicit real*8 (a-h,o-z)
1890 ! include 'DIMENSIONS'
1891 ! include 'COMMON.GEO'
1892 ! include 'COMMON.CHAIN'
1894 integer :: i1,i2,i3,i4
1895 real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1896 real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1897 real(kind=8) :: tx,ty,tz
1907 !d print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1908 !d print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1909 !d print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1913 wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1917 vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1918 if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1919 scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1920 if (dabs(scalar).gt.1.0D0) &
1921 scalar=0.99999999999999D0*scalar/dabs(scalar)
1923 !d print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1928 ! if (angle.le.0.0D0) angle=pi+angle
1932 scalar=tx*x23+ty*y23+tz*z23
1933 if (scalar.lt.0.0D0) angle=-angle
1937 !-----------------------------------------------------------------------------
1938 real(kind=8) function dist(i1,i2)
1940 ! Calculates the distance between atoms (i1) and (i2).
1942 ! implicit real*8 (a-h,o-z)
1943 ! include 'DIMENSIONS'
1944 ! include 'COMMON.GEO'
1945 ! include 'COMMON.CHAIN'
1948 real(kind=8) :: x12,y12,z12
1952 dist=dsqrt(x12*x12+y12*y12+z12*z12)
1955 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1956 !-----------------------------------------------------------------------------
1958 !-----------------------------------------------------------------------------
1959 subroutine local_move_init(debug)
1963 ! implicit real*8 (a-h,o-z)
1964 ! include 'DIMENSIONS' ! Needed by COMMON.LOCAL
1965 ! include 'COMMON.GEO' ! For pi, deg2rad
1966 ! include 'COMMON.LOCAL' ! For vbl
1967 ! include 'COMMON.LOCMOVE'
1973 ! Determine wheter to do some debugging output
1974 locmove_output=debug
1976 ! Set the init_called flag to 1
1979 ! The following are never changed
1980 min_theta=60.D0*deg2rad ! (0,PI)
1981 max_theta=175.D0*deg2rad ! (0,PI)
1982 dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1983 dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1986 small2=0.5*small*small
1988 ! Not really necessary...
1994 end subroutine local_move_init
1995 !-----------------------------------------------------------------------------
1996 subroutine local_move(n_start, n_end, PHImin, PHImax)
1997 ! Perform a local move between residues m and n (inclusive)
1998 ! PHImin and PHImax [0,PI] determine the size of the move
1999 ! Works on whatever structure is in the variables theta and phi,
2000 ! sidechain variables are left untouched
2001 ! The final structure is NOT minimized, but both the cartesian
2002 ! variables c and the angles are up-to-date at the end (no further
2003 ! chainbuild is required)
2005 use random,only:ran_number
2007 ! implicit real*8 (a-h,o-z)
2008 ! include 'DIMENSIONS'
2009 ! include 'COMMON.GEO'
2010 ! include 'COMMON.CHAIN'
2011 ! include 'COMMON.VAR'
2012 ! include 'COMMON.MINIM'
2013 ! include 'COMMON.SBRIDGE'
2014 ! include 'COMMON.LOCMOVE'
2016 ! External functions
2017 !EL integer move_res
2018 !EL external move_res
2019 !EL double precision ran_number
2020 !EL external ran_number
2023 integer :: n_start, n_end ! First and last residues to move
2024 real(kind=8) :: PHImin, PHImax ! min/max angles [0,PI]
2028 real(kind=8) :: min,max
2032 ! Check if local_move_init was called. This assumes that it
2033 ! would not be 1 if not explicitely initialized
2034 if (init_called.ne.1) then
2035 write(6,*)' *** local_move_init not called!!!'
2039 ! Quick check for crazy range
2040 if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2041 write(6,'(a,i3,a,i3)') &
2042 ' *** Cannot make local move between n_start = ',&
2043 n_start,' and n_end = ',n_end
2047 ! Take care of end residues first...
2048 if (n_start.eq.1) then
2049 ! Move residue 1 (completely random)
2050 theta(3)=ran_number(min_theta,max_theta)
2051 phi(4)=ran_number(-PI,PI)
2056 if (n_end.eq.nres) then
2057 ! Move residue nres (completely random)
2058 theta(nres)=ran_number(min_theta,max_theta)
2059 phi(nres)=ran_number(-PI,PI)
2065 ! ...then go through all other residues one by one
2066 ! Start from the two extremes and converge
2071 !$$$c Move the first two residues by less than the others
2072 !$$$ if (i-n_start.lt.3) then
2073 !$$$ if (i-n_start.eq.0) then
2076 !$$$ else if (i-n_start.eq.1) then
2079 !$$$ else if (i-n_start.eq.2) then
2085 ! The actual move, on residue i
2086 iretcode=move_res(min,max,i) ! Discard iretcode
2092 !$$$c Move the last two residues by less than the others
2093 !$$$ if (n_end-j.lt.3) then
2094 !$$$ if (n_end-j.eq.0) then
2097 !$$$ else if (n_end-j.eq.1) then
2100 !$$$ else if (n_end-j.eq.2) then
2106 ! The actual move, on residue j
2107 iretcode=move_res(min,max,j) ! Discard iretcode
2112 call int_from_cart(.false.,.false.)
2115 end subroutine local_move
2116 !-----------------------------------------------------------------------------
2117 subroutine output_tabs
2118 ! Prints out the contents of a_..., b_..., res_...
2122 ! include 'COMMON.GEO'
2123 ! include 'COMMON.LOCMOVE'
2129 write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2130 write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2133 write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2134 write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2137 write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2138 write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2139 write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2140 write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2143 end subroutine output_tabs
2144 !-----------------------------------------------------------------------------
2145 subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2146 ! Only uses angles if [0,PI] (but PHImin cannot be 0.,
2147 ! and PHImax cannot be PI)
2151 ! include 'COMMON.GEO'
2154 real(kind=8) :: PHImin,PHImax
2158 real(kind=8),dimension(0:3) :: ang
2159 logical,dimension(0:2,0:3) :: tab
2162 if (PHImin .eq. PHImax) then
2163 ! Special case with two 010's
2173 else if (PHImin .eq. PI) then
2174 ! Special case with one 010
2180 else if (PHImax .eq. 0.) then
2181 ! Special case with one 010
2190 if (PHImin .gt. 0.) then
2191 ! Start of range (011)
2196 ! End of range (110)
2200 tab(2,n+1) = .false.
2203 if (PHImax .lt. PI) then
2204 ! Start of range (011)
2209 ! End of range (110)
2213 tab(2,n+1) = .false.
2219 end subroutine angles2tab
2220 !-----------------------------------------------------------------------------
2221 subroutine minmax_angles(x,y,z,r,n,ang,tab)
2222 ! When solutions do not exist, assume all angles
2223 ! are acceptable - i.e., initial geometry must be correct
2227 ! include 'COMMON.GEO'
2228 ! include 'COMMON.LOCMOVE'
2231 real(kind=8) :: x,y,z,r
2235 real(kind=8),dimension(0:3) :: ang
2236 logical,dimension(0:2,0:3) :: tab
2239 real(kind=8) :: num, denom, phi
2240 real(kind=8) :: Kmin, Kmax
2244 num = x*x + y*y + z*z
2247 if (denom .gt. 0.) then
2249 denom = 2.*r*sqrt(denom)
2251 Kmin = (num - dmin2)/denom
2252 Kmax = (num - dmax2)/denom
2254 ! Allowed values of K (else all angles are acceptable)
2257 if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2259 else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2265 if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2267 else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2273 if (Kmax .lt. Kmin) Kmax = Kmin
2275 call angles2tab(Kmin, Kmax, n, ang, tab)
2277 ! Add phi and check that angles are within range (-PI,PI]
2280 if (ang(i) .le. -PI) then
2281 ang(i) = ang(i)+2.*PI
2282 else if (ang(i) .gt. PI) then
2283 ang(i) = ang(i)-2.*PI
2289 end subroutine minmax_angles
2290 !-----------------------------------------------------------------------------
2291 subroutine construct_tab
2292 ! Take a_... and b_... values and produces the results res_...
2293 ! x_ang are assumed to be all different (diff > small)
2294 ! x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2298 ! include 'COMMON.LOCMOVE'
2301 integer :: n_max,i,j,index
2307 if (n_max .eq. 0) then
2314 res_tab(j,0,i) = .true.
2315 res_tab(j,2,i) = .true.
2316 res_tab(j,1,i) = .false.
2323 do while (.not.done)
2324 res_ang(index) = flag
2328 if ((a_ang(i)-phi).gt.small .and. &
2329 a_ang(i) .lt. res_ang(index)) then
2330 ! Found a lower angle
2331 res_ang(index) = a_ang(i)
2332 ! Copy the values from a_tab into res_tab(0,,)
2333 res_tab(0,0,index) = a_tab(0,i)
2334 res_tab(0,1,index) = a_tab(1,i)
2335 res_tab(0,2,index) = a_tab(2,i)
2336 ! Set default values for res_tab(1,,)
2337 res_tab(1,0,index) = .true.
2338 res_tab(1,1,index) = .false.
2339 res_tab(1,2,index) = .true.
2340 else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2341 ! Found an equal angle (can only be equal to a b_ang)
2342 res_tab(0,0,index) = a_tab(0,i)
2343 res_tab(0,1,index) = a_tab(1,i)
2344 res_tab(0,2,index) = a_tab(2,i)
2349 if ((b_ang(i)-phi).gt.small .and. &
2350 b_ang(i) .lt. res_ang(index)) then
2351 ! Found a lower angle
2352 res_ang(index) = b_ang(i)
2353 ! Copy the values from b_tab into res_tab(1,,)
2354 res_tab(1,0,index) = b_tab(0,i)
2355 res_tab(1,1,index) = b_tab(1,i)
2356 res_tab(1,2,index) = b_tab(2,i)
2357 ! Set default values for res_tab(0,,)
2358 res_tab(0,0,index) = .true.
2359 res_tab(0,1,index) = .false.
2360 res_tab(0,2,index) = .true.
2361 else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2362 ! Found an equal angle (can only be equal to an a_ang)
2363 res_tab(1,0,index) = b_tab(0,i)
2364 res_tab(1,1,index) = b_tab(1,i)
2365 res_tab(1,2,index) = b_tab(2,i)
2369 if (res_ang(index) .eq. flag) then
2372 else if (index .eq. n_max-1) then
2376 phi = res_ang(index) ! Store previous angle
2384 if (a_n .gt. 0) then
2385 do while (.not.res_tab(0,1,index))
2388 done = res_tab(0,2,index)
2389 do i=index+1,res_n-1
2390 if (res_tab(0,1,i)) then
2391 done = res_tab(0,2,i)
2393 res_tab(0,0,i) = done
2394 res_tab(0,1,i) = done
2395 res_tab(0,2,i) = done
2398 done = res_tab(0,0,index)
2400 if (res_tab(0,1,i)) then
2401 done = res_tab(0,0,i)
2403 res_tab(0,0,i) = done
2404 res_tab(0,1,i) = done
2405 res_tab(0,2,i) = done
2410 res_tab(0,0,i) = .true.
2411 res_tab(0,1,i) = .true.
2412 res_tab(0,2,i) = .true.
2417 if (b_n .gt. 0) then
2418 do while (.not.res_tab(1,1,index))
2421 done = res_tab(1,2,index)
2422 do i=index+1,res_n-1
2423 if (res_tab(1,1,i)) then
2424 done = res_tab(1,2,i)
2426 res_tab(1,0,i) = done
2427 res_tab(1,1,i) = done
2428 res_tab(1,2,i) = done
2431 done = res_tab(1,0,index)
2433 if (res_tab(1,1,i)) then
2434 done = res_tab(1,0,i)
2436 res_tab(1,0,i) = done
2437 res_tab(1,1,i) = done
2438 res_tab(1,2,i) = done
2443 res_tab(1,0,i) = .true.
2444 res_tab(1,1,i) = .true.
2445 res_tab(1,2,i) = .true.
2449 ! Finally fill the last row with AND operation
2452 res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2457 end subroutine construct_tab
2458 !-----------------------------------------------------------------------------
2459 subroutine construct_ranges(phi_n,phi_start,phi_end)
2460 ! Given the data in res_..., construct a table of
2461 ! min/max allowed angles
2465 ! include 'COMMON.GEO'
2466 ! include 'COMMON.LOCMOVE'
2470 real(kind=8),dimension(0:11) :: phi_start,phi_end
2477 if (res_n .eq. 0) then
2478 ! Any move is allowed
2486 do while (.not.done)
2487 ! Find start of range (01x)
2489 do while (.not.done)
2490 if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2494 phi_start(phi_n) = res_ang(index)
2496 if (index .eq. res_n) done = .true.
2498 ! If a start was found (index < res_n), find the end of range (x10)
2499 ! It may not be found without wrapping around
2500 if (index .lt. res_n) then
2502 do while (.not.done)
2503 if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2508 if (index .eq. res_n) done = .true.
2510 if (index .lt. res_n) then
2511 ! Found the end of the range
2512 phi_end(phi_n) = res_ang(index)
2515 if (index .eq. res_n) then
2521 ! Need to wrap around
2523 phi_end(phi_n) = flag
2527 ! Take care of the last one if need to wrap around
2528 if (phi_end(phi_n) .eq. flag) then
2530 do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2533 phi_end(phi_n) = res_ang(index) + 2.*PI
2539 end subroutine construct_ranges
2540 !-----------------------------------------------------------------------------
2541 subroutine fix_no_moves(phi)
2545 ! include 'COMMON.GEO'
2546 ! include 'COMMON.LOCMOVE'
2553 real(kind=8) :: diff,temp
2556 ! Look for first 01x in gammas (there MUST be at least one)
2559 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2562 if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2563 ! Try to increase PHImax
2564 if (index .gt. 0) then
2565 phi = res_ang(index-1)
2566 diff = abs(res_ang(index) - res_ang(index-1))
2568 ! Look for last (corresponding) x10
2570 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2573 if (index .lt. res_n-1) then
2574 temp = abs(res_ang(index) - res_ang(index+1))
2575 if (temp .lt. diff) then
2576 phi = res_ang(index+1)
2582 ! If increasing PHImax didn't work, decreasing PHImin
2583 ! will (with one exception)
2584 ! Look for first x10 (there MUST be at least one)
2586 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2589 if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2590 ! Try to decrease PHImin
2591 if (index .lt. res_n-1) then
2592 temp = abs(res_ang(index) - res_ang(index+1))
2593 if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2594 phi = res_ang(index+1)
2598 ! Look for last (corresponding) 01x
2600 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2603 if (index .gt. 0) then
2604 temp = abs(res_ang(index) - res_ang(index-1))
2605 if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2606 phi = res_ang(index-1)
2612 ! If it still didn't work, it must be PHImax == 0. or PHImin == PI
2613 if (diff .eq. flag) then
2615 if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2616 res_tab(index,1,2)) index = res_n - 1
2617 ! This MUST work at this point
2618 if (index .eq. 0) then
2621 phi = res_ang(index - 1)
2626 end subroutine fix_no_moves
2627 !-----------------------------------------------------------------------------
2628 integer function move_res(PHImin,PHImax,i_move)
2629 ! Moves residue i_move (in array c), leaving everything else fixed
2630 ! Starting geometry is not checked, it should be correct!
2631 ! R(,i_move) is the only residue that will move, but must have
2632 ! 1 < i_move < nres (i.e., cannot move ends)
2633 ! Whether any output is done is controlled by locmove_output
2635 use random,only:ran_number
2637 ! implicit real*8 (a-h,o-z)
2638 ! include 'DIMENSIONS'
2639 ! include 'COMMON.CHAIN'
2640 ! include 'COMMON.GEO'
2641 ! include 'COMMON.LOCMOVE'
2643 ! External functions
2644 !EL double precision ran_number
2645 !EL external ran_number
2648 real(kind=8) :: PHImin,PHImax
2652 ! 0: move successfull
2653 ! 1: Dmin or Dmax had to be modified
2654 ! 2: move failed - check your input geometry
2658 real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2659 real(kind=8),dimension(0:2) :: P
2660 logical :: no_moves,done
2661 integer :: index,i,j
2662 real(kind=8) :: phi,temp,radius
2663 real(kind=8),dimension(0:11) :: phi_start,phi_end
2666 ! Set up the coordinate system
2668 Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2672 Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2674 temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2680 X(i)=c(i+1,i_move)-Orig(i)
2682 ! radius is the radius of the circle on which c(,i_move) can move
2683 radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2688 Y(0)=Z(1)*X(2)-X(1)*Z(2)
2689 Y(1)=X(0)*Z(2)-Z(0)*X(2)
2690 Y(2)=Z(0)*X(1)-X(0)*Z(1)
2692 ! Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2693 if (i_move.gt.2) then
2695 P(i)=c(i+1,i_move-2)-Orig(i)
2697 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2698 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2699 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2700 radius,a_n,a_ang,a_tab)
2705 ! Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2706 if (i_move.lt.nres-2) then
2708 P(i)=c(i+1,i_move+2)-Orig(i)
2710 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2711 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2712 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2713 radius,b_n,b_ang,b_tab)
2718 ! Construct the resulting table for alpha and beta
2719 call construct_tab()
2721 if (locmove_output) then
2722 print *,'ALPHAS & BETAS TABLE'
2726 ! Check that there is at least one possible move
2728 if (res_n .eq. 0) then
2732 do while ((index .lt. res_n) .and. no_moves)
2733 if (res_tab(2,1,index)) no_moves = .false.
2738 if (locmove_output) print *,' *** Cannot move anywhere'
2743 ! Transfer res_... into a_...
2746 if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2747 (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2748 a_ang(a_n) = res_ang(i)
2750 a_tab(j,a_n) = res_tab(2,j,i)
2756 ! Check that the PHI's are within [0,PI]
2757 if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2758 if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2759 if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2760 if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2761 if (PHImax .lt. PHImin) PHImax = PHImin
2762 ! Calculate min and max angles coming from PHImin and PHImax,
2763 ! and put them in b_...
2764 call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2765 ! Construct the final table
2766 call construct_tab()
2768 if (locmove_output) then
2769 print *,'FINAL TABLE'
2773 ! Check that there is at least one possible move
2775 if (res_n .eq. 0) then
2779 do while ((index .lt. res_n) .and. no_moves)
2780 if (res_tab(2,1,index)) no_moves = .false.
2786 ! Take care of the case where no solution exists...
2787 call fix_no_moves(phi)
2788 if (locmove_output) then
2789 print *,' *** Had to modify PHImin or PHImax'
2790 print *,'phi: ',phi*rad2deg
2794 ! ...or calculate the solution
2795 ! Construct phi_start/phi_end arrays
2796 call construct_ranges(phi_n, phi_start, phi_end)
2797 ! Choose random angle phi in allowed range(s)
2800 temp = temp + phi_end(i) - phi_start(i)
2802 phi = ran_number(phi_start(0),phi_start(0)+temp)
2805 do while (.not.done)
2806 if (phi .lt. phi_end(index)) then
2811 if (index .eq. phi_n) then
2813 else if (.not.done) then
2814 phi = phi + phi_start(index) - phi_end(index-1)
2817 if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2818 if (phi .gt. PI) phi = phi-2.*PI
2820 if (locmove_output) then
2821 print *,'ALLOWED RANGE(S)'
2823 print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2825 print *,'phi: ',phi*rad2deg
2830 ! Re-use radius as temp variable
2831 temp=radius*cos(phi)
2832 radius=radius*sin(phi)
2834 c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2838 end function move_res
2839 !-----------------------------------------------------------------------------
2844 ! implicit real*8 (a-h,o-z)
2845 ! include 'DIMENSIONS'
2846 ! include 'COMMON.GEO'
2847 ! include 'COMMON.LOCAL'
2848 ! include 'COMMON.LOCMOVE'
2850 ! External functions
2851 !EL integer move_res
2852 !EL external move_res
2857 real(kind=8),dimension(0:11) :: phi_start,phi_end
2859 real(kind=8),dimension(0:2,0:5) :: R
2861 locmove_output=.true.
2863 ! call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2864 ! call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2865 ! call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2866 ! call construct_tab
2869 ! call construct_ranges(phi_n,phi_start,phi_end)
2871 ! print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2874 ! call fix_no_moves(phi)
2875 ! print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2881 R(1,1)=-cos(28.D0*deg2rad)
2882 R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2886 R(0,3)=cos(30.D0*deg2rad)
2893 R(1,5)=cos(26.D0*deg2rad)
2894 R(2,5)=0.5D0+sin(26.D0*deg2rad)
2900 ! i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2902 i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2903 print *,'RETURNED ',i
2904 print *,(R(i,3)/vbl,i=0,2)
2907 end subroutine loc_test
2909 !-----------------------------------------------------------------------------
2911 !-----------------------------------------------------------------------------
2912 subroutine MATMULT(A1,A2,A3)
2913 ! implicit real*8 (a-h,o-z)
2914 ! include 'DIMENSIONS'
2917 real(kind=8) :: A3IJ
2919 real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2920 real(kind=8),DIMENSION(3,3) :: AI3
2925 3 A3IJ=A3IJ+A1(I,K)*A2(K,J)
2933 end subroutine MATMULT
2934 !-----------------------------------------------------------------------------
2936 !-----------------------------------------------------------------------------
2937 subroutine int_from_cart(lside,lprn)
2938 ! implicit real*8 (a-h,o-z)
2939 ! include 'DIMENSIONS'
2940 use control_data,only:out1file
2944 ! include 'COMMON.LOCAL'
2945 ! include 'COMMON.VAR'
2946 ! include 'COMMON.CHAIN'
2947 ! include 'COMMON.INTERACT'
2948 ! include 'COMMON.IOUNITS'
2949 ! include 'COMMON.GEO'
2950 ! include 'COMMON.NAMES'
2951 ! include 'COMMON.CONTROL'
2952 ! include 'COMMON.SETUP'
2953 character(len=3) :: seq,res
2955 character(len=80) :: card
2956 real(kind=8),dimension(3,20) :: sccor
2957 integer :: i,j,iti !el rescode,
2958 logical :: lside,lprn
2959 real(kind=8) :: di,cosfac,sinfac
2963 if(me.eq.king.or..not.out1file)then
2965 write (iout,'(/a)') &
2966 'Internal coordinates calculated from crystal structure.'
2968 write (iout,'(8a)') ' Res ',' dvb',' Theta',&
2969 ' Gamma',' Dsc_id',' Dsc',' Alpha',&
2972 write (iout,'(4a)') ' Res ',' dvb',' Theta',&
2978 ! if (molnum(i).ne.1) cycle
2979 !in wham do i=1,nres
2981 if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2982 (iti.ne.ntyp1 .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2983 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2987 vbld(i+1)=dist(i,i+1)
2988 vbld_inv(i+1)=1.0d0/vbld(i+1)
2990 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2991 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2995 ! if (itype(1,1).eq.ntyp1) then
2997 ! c(j,1)=c(j,2)+(c(j,3)-c(j,4))
3000 ! if (itype(nres,1).eq.ntyp1) then
3002 ! c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
3006 ! if (unres_pdb) then
3007 ! if (itype(1,1).eq.21) then
3008 ! theta(3)=90.0d0*deg2rad
3009 ! phi(4)=180.0d0*deg2rad
3011 ! vbld_inv(2)=1.0d0/vbld(2)
3013 ! if (itype(nres,1).eq.21) then
3014 ! theta(nres)=90.0d0*deg2rad
3015 ! phi(nres)=180.0d0*deg2rad
3017 ! vbld_inv(nres)=1.0d0/vbld(2)
3023 c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
3024 +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
3025 ! in wham c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
3030 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3032 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3033 di=dsc(itype(i,molnum(i)))
3035 if (itype(i,1).ne.10) then
3036 vbld_inv(i+nres)=1.0d0/di
3038 vbld_inv(i+nres)=0.0d0
3042 alph(i)=alpha(nres+i,i,nres2+2)
3043 omeg(i)=beta(nres+i,i,nres2+2,i+1)
3046 if(me.eq.king.or..not.out1file)then
3048 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3049 rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3050 rad2deg*alph(i),rad2deg*omeg(i)
3053 if(me.eq.king.or..not.out1file)then
3055 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3056 rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3057 rad2deg*alph(i),rad2deg*omeg(i)
3064 if(me.eq.king.or..not.out1file) &
3065 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3066 rad2deg*theta(i),rad2deg*phi(i)
3070 end subroutine int_from_cart
3071 !-----------------------------------------------------------------------------
3072 subroutine sc_loc_geom(lprn)
3073 ! implicit real*8 (a-h,o-z)
3074 ! include 'DIMENSIONS'
3075 use control_data,only:out1file
3079 ! include 'COMMON.LOCAL'
3080 ! include 'COMMON.VAR'
3081 ! include 'COMMON.CHAIN'
3082 ! include 'COMMON.INTERACT'
3083 ! include 'COMMON.IOUNITS'
3084 ! include 'COMMON.GEO'
3085 ! include 'COMMON.NAMES'
3086 ! include 'COMMON.CONTROL'
3087 ! include 'COMMON.SETUP'
3088 real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3091 integer :: i,j,it,iti
3092 real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3095 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3099 if (itype(i,1).ne.10) then
3101 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3105 dc_norm(j,i+nres)=0.0d0
3110 costtab(i+1) =dcos(theta(i+1))
3111 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3112 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3113 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3114 cosfac2=0.5d0/(1.0d0+costtab(i+1))
3115 cosfac=dsqrt(cosfac2)
3116 sinfac2=0.5d0/(1.0d0-costtab(i+1))
3117 sinfac=dsqrt(sinfac2)
3120 if ((it.ne.10).and.(it.ne.ntyp1)) then
3121 !el if (it.ne.10) then
3123 ! Compute the axes of tghe local cartesian coordinates system; store in
3124 ! x_prime, y_prime and z_prime
3132 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3133 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3135 call vecpr(x_prime,y_prime,z_prime)
3137 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3138 ! to local coordinate system. Store in xx, yy, zz.
3144 xx = xx + x_prime(j)*dc_norm(j,i+nres)
3145 yy = yy + y_prime(j)*dc_norm(j,i+nres)
3146 zz = zz + z_prime(j)*dc_norm(j,i+nres)
3161 if(me.eq.king.or..not.out1file) &
3162 write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3168 end subroutine sc_loc_geom
3169 !-----------------------------------------------------------------------------
3170 subroutine sccenter(ires,nscat,sccor)
3171 ! implicit real*8 (a-h,o-z)
3172 ! include 'DIMENSIONS'
3173 ! include 'COMMON.CHAIN'
3174 integer :: i,j,ires,nscat
3175 real(kind=8),dimension(3,20) :: sccor
3176 real(kind=8) :: sccmj
3177 ! print *,"I am in sccenter",ires,nscat
3181 sccmj=sccmj+sccor(j,i)
3182 !C print *,"insccent", ires,sccor(j,i)
3184 dc(j,ires)=sccmj/nscat
3187 end subroutine sccenter
3188 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3189 !-----------------------------------------------------------------------------
3190 subroutine bond_regular
3192 ! implicit real*8 (a-h,o-z)
3193 ! include 'DIMENSIONS'
3194 ! include 'COMMON.VAR'
3195 ! include 'COMMON.LOCAL'
3196 ! include 'COMMON.CALC'
3197 ! include 'COMMON.INTERACT'
3198 ! include 'COMMON.CHAIN'
3202 vbld_inv(i+1)=1.0d0/vbld(i+1)
3203 vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3204 vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3205 ! print *,vbld(i+1),vbld(i+1+nres)
3208 end subroutine bond_regular
3210 !-----------------------------------------------------------------------------
3212 !-----------------------------------------------------------------------------
3213 subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3214 ! This subroutine calculates unit vectors of a local reference system
3215 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3216 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3217 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3218 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3219 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3220 ! form a linear fragment. Returns vectors e1, e2, and e3.
3221 ! implicit real*8 (a-h,o-z)
3222 ! include 'DIMENSIONS'
3224 real(kind=8),dimension(3) :: e1,e2,e3
3225 real(kind=8),dimension(3) :: u,z
3226 ! include 'COMMON.IOUNITS'
3227 ! include 'COMMON.CHAIN'
3228 real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3230 integer :: i,i1,i2,i3,i4
3231 real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3244 if (s1.gt.coinc) goto 2
3245 write (iout,1000) i2,i3,i1
3250 2 if (s2.gt.coinc) goto 4
3251 write(iout,1000) i3,i4,i1
3258 v1=z(2)*u(3)-z(3)*u(2)
3259 v2=z(3)*u(1)-z(1)*u(3)
3260 v3=z(1)*u(2)-z(2)*u(1)
3261 anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3262 if (anorm.gt.align) goto 6
3263 write (iout,1010) i2,i3,i4,i1
3275 e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3276 e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3277 e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3278 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3279 'coordinates of atom',i4,' are set to zero.')
3280 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3281 ' fragment. coordinates of atom',i4,' are set to zero.')
3283 end subroutine refsys
3284 !-----------------------------------------------------------------------------
3286 !-----------------------------------------------------------------------------
3287 subroutine int_to_cart
3288 !--------------------------------------------------------------
3289 ! This subroutine converts the energy derivatives from internal
3290 ! coordinates to cartesian coordinates
3291 !-------------------------------------------------------------
3292 ! implicit real*8 (a-h,o-z)
3293 ! include 'DIMENSIONS'
3294 ! include 'COMMON.VAR'
3295 ! include 'COMMON.CHAIN'
3296 ! include 'COMMON.DERIV'
3297 ! include 'COMMON.GEO'
3298 ! include 'COMMON.LOCAL'
3299 ! include 'COMMON.INTERACT'
3300 ! include 'COMMON.MD'
3301 ! include 'COMMON.IOUNITS'
3302 ! include 'COMMON.SCCOR'
3303 ! calculating dE/ddc1
3306 ! print *,"gloc",gloc(:,:)
3307 ! print *, "gcart",gcart(:,:)
3308 if (nres.lt.3) go to 18
3310 gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3311 +gloc(nres-2,icg)*dtheta(j,1,3)
3312 if ((itype(2,1).ne.10).and.&
3313 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3314 gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3315 gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3318 ! Calculating the remainder of dE/ddc2
3320 gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3321 gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3322 if(itype(2,1).ne.10) then
3323 gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3324 gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3326 if(itype(3,1).ne.10) then
3327 gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3328 gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3331 gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3334 ! If there are only five residues
3337 gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3338 dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3340 ! if(itype(3,1).ne.10) then
3341 if ((itype(3,1).ne.10).and.&
3342 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3343 gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3344 dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3346 ! if(itype(4,1).ne.10) then
3347 if ((itype(4,1).ne.10).and.&
3348 (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3349 gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3350 dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3354 ! If there are more than five residues
3358 gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3359 +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3360 gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3361 gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3362 if(itype(i,1).ne.10) then
3363 gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3364 gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3366 if(itype(i+1,1).ne.10) then
3367 gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3368 +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3373 ! Setting dE/ddnres-2
3376 gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3377 dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3378 +gloc(2*nres-6,icg)* &
3379 dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3380 if(itype(nres-2,1).ne.10) then
3381 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3382 dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3385 if(itype(nres-1,1).ne.10) then
3386 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3387 dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3392 ! Settind dE/ddnres-1
3396 write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3397 gloc(2*nres-5,icg),dtheta(j,2,nres)
3403 gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3404 gloc(2*nres-5,icg)*dtheta(j,2,nres)
3407 write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3408 gloc(2*nres-5,icg),dtheta(j,2,nres)
3412 if(itype(nres-1,1).ne.10) then
3413 gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3414 dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3418 write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3419 dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3427 ! The side-chain vector derivatives
3429 if(itype(i,1).ne.10 .and. &
3430 itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3432 gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3433 +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3436 write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3437 gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3443 !----------------------------------------------------------------------
3444 ! INTERTYP=1 SC...Ca...Ca...Ca
3445 ! INTERTYP=2 Ca...Ca...Ca...SC
3446 ! INTERTYP=3 SC...Ca...Ca...SC
3447 ! calculating dE/ddc1
3451 ! write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3453 if (nres.lt.2) return
3454 if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3455 if ((itype(1,1).ne.10).and. &
3456 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3458 !c Derviative was calculated for oposite vector of side chain therefore
3459 ! there is "-" sign before gloc_sc
3460 gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3462 gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3464 if ((itype(2,1).ne.10).and. &
3465 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3466 gxcart(j,1)= gxcart(j,1) &
3467 -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3468 gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3473 if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3474 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3477 gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3480 ! As potetnial DO NOT depend on omicron anlge their derivative is
3482 ! & +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3484 ! Calculating the remainder of dE/ddc2
3486 if((itype(2,1).ne.10).and. &
3487 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3488 if ((itype(1,1).ne.10).and.&
3489 ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3490 gxcart(j,2)=gxcart(j,2)+ &
3491 gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3492 if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3494 gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3495 !c the - above is due to different vector direction
3496 gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3499 ! if ((itype(1,1).ne.10).and.&
3500 ! ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3501 gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3502 !c the - above is due to different vector direction
3503 gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3504 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3505 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3508 if ((itype(1,1).ne.10).and.&
3509 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3510 gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3511 ! write(iout,*) gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3513 if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3514 gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3515 ! write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3517 if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3518 gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3519 ! write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3522 ! write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3524 ! If there are more than five residues
3528 ! write(iout,*) "before", gcart(j,i)
3529 if ((itype(i,1).ne.10).and.&
3530 (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3531 gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3532 *dtauangle(j,2,3,i+1) &
3533 -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3534 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3535 *dtauangle(j,1,2,i+2)
3536 ! write(iout,*) "new",j,i,
3537 ! & gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3538 ! if (itype(i-1,1).ne.10) then
3539 if ((itype(i-1,1).ne.10).and.&
3540 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3542 gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3543 *dtauangle(j,3,3,i+1)
3545 ! if (itype(i+1,1).ne.10) then
3546 if ((itype(i+1,1).ne.10).and.&
3547 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3548 gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3549 *dtauangle(j,3,1,i+2)
3550 gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3551 *dtauangle(j,3,2,i+2)
3554 ! if (itype(i-1,1).ne.10) then
3555 if ((itype(i-1,1).ne.10).and.&
3556 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3557 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3558 dtauangle(j,1,3,i+1)
3560 ! if (itype(i+1,1).ne.10) then
3561 if ((itype(i+1,1).ne.10).and.&
3562 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3563 gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3564 dtauangle(j,2,2,i+2)
3565 ! write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3566 ! & dtauangle(j,2,2,i+2)
3568 ! if (itype(i+2,1).ne.10) then
3569 if ((itype(i+2,1).ne.10).and.&
3570 (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3571 gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3572 dtauangle(j,2,1,i+3)
3577 ! Setting dE/ddnres-1
3580 if ((itype(nres-1,1).ne.10).and.&
3581 (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3582 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3583 *dtauangle(j,2,3,nres)
3584 ! write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3585 ! & dtauangle(j,2,3,nres), gxcart(j,nres-1)
3586 ! if (itype(nres-2,1).ne.10) then
3587 if ((itype(nres-2,1).ne.10).and.&
3588 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3589 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3590 *dtauangle(j,3,3,nres)
3592 if ((itype(nres,1).ne.10).and.&
3593 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3594 gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3595 *dtauangle(j,3,1,nres+1)
3596 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3597 *dtauangle(j,3,2,nres+1)
3600 if ((itype(nres-2,1).ne.10).and.&
3601 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3602 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3603 dtauangle(j,1,3,nres)
3605 if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3606 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3607 dtauangle(j,2,2,nres+1)
3608 ! write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3609 ! & dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3614 if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3615 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3617 gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3618 *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3619 *dtauangle(j,2,3,nres+1)
3622 ! The side-chain vector derivatives
3623 ! print *,"gcart",gcart(:,:)
3625 end subroutine int_to_cart
3626 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3627 !-----------------------------------------------------------------------------
3629 !-----------------------------------------------------------------------------
3630 subroutine gen_dist_constr
3631 ! Generate CA distance constraints.
3632 ! implicit real*8 (a-h,o-z)
3633 ! include 'DIMENSIONS'
3634 ! include 'COMMON.IOUNITS'
3635 ! include 'COMMON.GEO'
3636 ! include 'COMMON.VAR'
3637 ! include 'COMMON.INTERACT'
3638 ! include 'COMMON.LOCAL'
3639 ! include 'COMMON.NAMES'
3640 ! include 'COMMON.CHAIN'
3641 ! include 'COMMON.FFIELD'
3642 ! include 'COMMON.SBRIDGE'
3643 ! include 'COMMON.HEADER'
3644 ! include 'COMMON.CONTROL'
3645 ! include 'COMMON.DBASE'
3646 ! include 'COMMON.THREAD'
3647 ! include 'COMMON.TIME1'
3648 ! integer :: itype_pdb !(maxres)
3649 ! common /pizda/ itype_pdb(nres)
3650 character(len=2) :: iden
3653 !d print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3654 !d write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3655 !d & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3657 do i=nstart_sup,nstart_sup+nsup-1
3658 !d write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3659 !d & ' seq_pdb', restyp(itype_pdb(i))
3660 do j=i+2,nstart_sup+nsup-1
3662 ihpb(nhpb)=i+nstart_seq-nstart_sup
3663 jhpb(nhpb)=j+nstart_seq-nstart_sup
3665 dhpb(nhpb)=dist(i,j)
3668 !d write (iout,'(a)') 'Distance constraints:'
3673 !d if (ii.gt.nres) then
3678 !d write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3679 !d & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3680 !d & dhpb(i),forcon(i)
3682 ! deallocate(itype_pdb)
3685 end subroutine gen_dist_constr
3687 !-----------------------------------------------------------------------------
3689 !-----------------------------------------------------------------------------
3690 subroutine cartprint
3692 use geometry_data, only: c
3693 use energy_data, only: itype
3694 ! implicit real*8 (a-h,o-z)
3695 ! include 'DIMENSIONS'
3696 ! include 'COMMON.CHAIN'
3697 ! include 'COMMON.INTERACT'
3698 ! include 'COMMON.NAMES'
3699 ! include 'COMMON.IOUNITS'
3704 write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3705 c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3707 100 format (//' alpha-carbon coordinates ',&
3708 ' centroid coordinates'/ &
3709 ' ', 6X,'X',11X,'Y',11X,'Z',&
3710 10X,'X',11X,'Y',11X,'Z')
3711 110 format (a,'(',i3,')',6f12.5)
3713 end subroutine cartprint
3714 !-----------------------------------------------------------------------------
3715 !-----------------------------------------------------------------------------
3716 subroutine alloc_geo_arrays
3717 !EL Allocation of tables used by module energy
3719 integer :: i,j,nres2
3723 allocate(phibound(2,nres+2)) !(2,maxres)
3724 !----------------------
3726 ! common /chain/ in molread
3727 ! real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3728 ! real(kind=8),dimension(:,:),allocatable :: dc
3729 allocate(dc_old(3,0:nres2))
3730 ! if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3731 if(.not.allocated(dc_norm2)) then
3732 allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3736 !el if(.not.allocated(dc_norm))
3737 !elwrite(iout,*) "jestem w alloc geo 1"
3738 if(.not.allocated(dc_norm)) then
3739 allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3742 !elwrite(iout,*) "jestem w alloc geo 1"
3743 allocate(xloc(3,nres),xrot(3,nres))
3744 !elwrite(iout,*) "jestem w alloc geo 1"
3746 !elwrite(iout,*) "jestem w alloc geo 1"
3747 allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3749 allocate(t(3,3,nres),r(3,3,nres))
3750 allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3751 ! common /refstruct/
3752 if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3753 !elwrite(iout,*) "jestem w alloc geo 2"
3754 allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3755 if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3756 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3757 ! common /from_zscore/ in module.compare
3758 !----------------------
3760 ! Inverses of the actual virtual bond lengths
3761 ! common /invlen/ in io_conf: molread or readpdb
3762 ! real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3763 !----------------------
3765 ! Store the geometric variables in the following COMMON block.
3766 ! common /var/ in readpdb or ...
3767 if(.not.allocated(theta)) allocate(theta(nres+2))
3768 if(.not.allocated(phi)) allocate(phi(nres+2))
3769 if(.not.allocated(alph)) allocate(alph(nres+2))
3770 if(.not.allocated(omeg)) allocate(omeg(nres+2))
3771 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3772 if(.not.allocated(phiref)) allocate(phiref(nres+2))
3773 if(.not.allocated(costtab)) allocate(costtab(nres))
3774 if(.not.allocated(sinttab)) allocate(sinttab(nres))
3775 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3776 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3777 ! real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3778 allocate(omicron(2,nres+2)) !(2,maxres)
3779 allocate(tauangle(3,nres+2)) !(3,maxres)
3780 !elwrite(iout,*) "jestem w alloc geo 3"
3781 if(.not.allocated(xxtab)) allocate(xxtab(nres))
3782 if(.not.allocated(yytab)) allocate(yytab(nres))
3783 if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3784 if(.not.allocated(xxref)) allocate(xxref(nres))
3785 if(.not.allocated(yyref)) allocate(yyref(nres))
3786 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3787 allocate(ialph(nres,2)) !(maxres,2)
3790 allocate(ivar(4*nres2)) !(4*maxres2)
3792 #if defined(WHAM_RUN) || defined(CLUSTER)
3793 allocate(vbld(2*nres))
3795 allocate(vbld_inv(2*nres))
3800 end subroutine alloc_geo_arrays
3801 !-----------------------------------------------------------------------------
3802 !-----------------------------------------------------------------------------
3803 subroutine returnbox
3804 integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3805 integer :: chain_end,ireturnval
3806 real*8 :: difference
3807 !C change suggested by Ana - end
3811 !C write(*,*) 'initial', i,j,c(j,i)
3813 !C change suggested by Ana - begin
3815 !C change suggested by Ana -end
3818 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3819 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3821 if (allareout.eq.1) then
3822 ireturnval=int(c(j,i)/boxxsize)
3823 if (c(j,i).le.0) ireturnval=ireturnval-1
3824 do k=chain_beg,chain_end
3825 c(j,k)=c(j,k)-ireturnval*boxxsize
3826 c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3829 if (chain_beg.eq.1) &
3830 dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3831 !C Suggested by Ana -end
3836 if (int(c(j,i)/boxxsize).eq.0) allareout=0
3839 if (allareout.eq.1) then
3840 ireturnval=int(c(j,i)/boxxsize)
3841 if (c(j,i).le.0) ireturnval=ireturnval-1
3843 c(j,k)=c(j,k)-ireturnval*boxxsize
3844 c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3849 !C write(*,*) 'befor no jump', i,j,c(j,i)
3854 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3855 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3856 difference=abs(c(j,i-1)-c(j,i))
3857 !C print *,'diff', difference
3858 if (difference.gt.boxxsize/2.0) then
3859 if (c(j,i-1).gt.c(j,i)) then
3868 c(j,i)=c(j,i)+nojumpval*boxxsize
3869 c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3874 if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3875 difference=abs(c(j,i-1)-c(j,i))
3876 if (difference.gt.boxxsize/2.0) then
3877 if (c(j,i-1).gt.c(j,i)) then
3886 c(j,i)=c(j,i)+nojumpval*boxxsize
3887 c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3891 !C write(*,*) 'after no jump', i,j,c(j,i)
3895 !C suggesed by Ana begins
3901 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3902 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3904 if (allareout.eq.1) then
3905 ireturnval=int(c(j,i)/boxysize)
3906 if (c(j,i).le.0) ireturnval=ireturnval-1
3907 do k=chain_beg,chain_end
3908 c(j,k)=c(j,k)-ireturnval*boxysize
3909 c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3912 if (chain_beg.eq.1) &
3913 dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3914 !C Suggested by Ana -end
3919 if (int(c(j,i)/boxysize).eq.0) allareout=0
3922 if (allareout.eq.1) then
3923 ireturnval=int(c(j,i)/boxysize)
3924 if (c(j,i).le.0) ireturnval=ireturnval-1
3926 c(j,k)=c(j,k)-ireturnval*boxysize
3927 c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3933 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3934 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3935 difference=abs(c(j,i-1)-c(j,i))
3936 if (difference.gt.boxysize/2.0) then
3937 if (c(j,i-1).gt.c(j,i)) then
3946 c(j,i)=c(j,i)+nojumpval*boxysize
3947 c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3952 if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3953 .and. itype(i-1,mnum).eq.ntyp1) then
3954 difference=abs(c(j,i-1)-c(j,i))
3955 if (difference.gt.boxysize/2.0) then
3956 if (c(j,i-1).gt.c(j,i)) then
3965 c(j,i)=c(j,i)+nojumpval*boxysize
3966 c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3969 !C Suggested by Ana -begins
3971 !C Suggested by Ana -ends
3976 if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3977 .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3979 if (allareout.eq.1) then
3980 ireturnval=int(c(j,i)/boxysize)
3981 if (c(j,i).le.0) ireturnval=ireturnval-1
3982 do k=chain_beg,chain_end
3983 c(j,k)=c(j,k)-ireturnval*boxzsize
3984 c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3987 if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3988 !C Suggested by Ana -end
3993 if (int(c(j,i)/boxzsize).eq.0) allareout=0
3996 if (allareout.eq.1) then
3997 ireturnval=int(c(j,i)/boxzsize)
3998 if (c(j,i).le.0) ireturnval=ireturnval-1
4000 c(j,k)=c(j,k)-ireturnval*boxzsize
4001 c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
4007 if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4008 difference=abs(c(j,i-1)-c(j,i))
4009 if (difference.gt.(boxzsize/2.0)) then
4010 if (c(j,i-1).gt.c(j,i)) then
4019 c(j,i)=c(j,i)+nojumpval*boxzsize
4020 c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4025 if (itype(i,mnum).eq.ntyp1_molec(mnum) &
4026 .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4027 difference=abs(c(j,i-1)-c(j,i))
4028 if (difference.gt.boxzsize/2.0) then
4029 if (c(j,i-1).gt.c(j,i)) then
4038 c(j,i)=c(j,i)+nojumpval*boxzsize
4039 c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4042 if (molnum(i).eq.5) then
4043 c(1,i)=dmod(c(1,i),boxxsize)
4044 c(2,i)=dmod(c(2,i),boxysize)
4045 c(3,i)=dmod(c(3,i),boxzsize)
4046 c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4047 c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4048 c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4052 end subroutine returnbox
4053 !-------------------------------------------------------------------------------------------------------