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
87 ! Define the origin and orientation of the coordinate system and locate the
88 ! first three CA's and SC(2).
90 !elwrite(iout,*)"in chainbuild"
92 !elwrite(iout,*)"after orig_frame"
94 ! Build the alpha-carbon chain.
97 call locate_next_res(i)
99 !elwrite(iout,*)"after locate_next_res"
101 ! First and last SC must coincide with the corresponding CA.
105 dc_norm(j,nres+1)=0.0D0
106 dc(j,nres+nres)=0.0D0
107 dc_norm(j,nres+nres)=0.0D0
109 c(j,nres+nres)=c(j,nres)
112 ! Temporary diagnosis
117 write (iout,'(/a)') 'Recalculated internal coordinates'
120 c(j,nres2)=0.5D0*(c(j,i-1)+c(j,i+1)) !maxres2=2*maxres
123 if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
124 be1=rad2deg*beta(nres+i,i,nres2,i+1)
126 if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
127 write (iout,1212) restyp(itype(i)),i,dist(i-1,i),&
128 alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,nres2),be1
130 1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
135 end subroutine chainbuild
136 !-----------------------------------------------------------------------------
137 subroutine orig_frame
139 ! Define the origin and orientation of the coordinate system and locate
140 ! the first three atoms.
142 ! implicit real*8 (a-h,o-z)
143 ! include 'DIMENSIONS'
144 ! include 'COMMON.CHAIN'
145 ! include 'COMMON.LOCAL'
146 ! include 'COMMON.GEO'
147 ! include 'COMMON.VAR'
150 real(kind=8) :: cost,sint
152 !el allocate(t(3,3,nres)) !(3,3,maxres)
153 !el allocate(r(3,3,nres)) !(3,3,maxres)
154 !el allocate(rt(3,3,nres)) !(3,3,maxres)
155 !el allocate(dc_norm(3,0:2*nres)) !(3,0:maxres2)
156 !el allocate(prod(3,3,nres)) !(3,3,maxres)
209 dc_norm(j,2)=prod(j,1,2)
210 dc(j,2)=vbld(3)*prod(j,1,2)
211 c(j,3)=c(j,2)+dc(j,2)
213 call locate_side_chain(2)
215 end subroutine orig_frame
216 !-----------------------------------------------------------------------------
217 subroutine locate_next_res(i)
219 ! Locate CA(i) and SC(i-1)
221 ! implicit real*8 (a-h,o-z)
222 ! include 'DIMENSIONS'
223 ! include 'COMMON.CHAIN'
224 ! include 'COMMON.LOCAL'
225 ! include 'COMMON.GEO'
226 ! include 'COMMON.VAR'
227 ! include 'COMMON.IOUNITS'
228 ! include 'COMMON.NAMES'
229 ! include 'COMMON.INTERACT'
231 ! Define the rotation matrices corresponding to CA(i)
235 real(kind=8) :: theti,phii
236 real(kind=8) :: cost,sint,cosphi,sinphi
241 call proc_proc(theti,icrc)
242 if(icrc.eq.1)theti=100.0
245 call proc_proc(phii,icrc)
246 if(icrc.eq.1)phii=180.0
249 if (theti.ne.theti) theti=100.0
251 if (phii.ne.phii) phii=180.0
261 ! Define the matrices of the rotation about the virtual-bond valence angles
262 ! theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
263 ! program), R(i,j,k), and, the cumulative matrices of rotation RT
285 rt(2,1,i-2)=sint*cosphi
286 rt(2,2,i-2)=-cost*cosphi
288 rt(3,1,i-2)=-sint*sinphi
289 rt(3,2,i-2)=cost*sinphi
291 call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
293 dc_norm(j,i-1)=prod(j,1,i-1)
294 dc(j,i-1)=vbld(i)*prod(j,1,i-1)
295 c(j,i)=c(j,i-1)+dc(j,i-1)
297 !d print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
299 ! Now calculate the coordinates of SC(i-1)
301 call locate_side_chain(i-1)
303 end subroutine locate_next_res
304 !-----------------------------------------------------------------------------
305 subroutine locate_side_chain(i)
307 ! Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
309 ! implicit real*8 (a-h,o-z)
310 ! include 'DIMENSIONS'
311 ! include 'COMMON.CHAIN'
312 ! include 'COMMON.LOCAL'
313 ! include 'COMMON.GEO'
314 ! include 'COMMON.VAR'
315 ! include 'COMMON.IOUNITS'
316 ! include 'COMMON.NAMES'
317 ! include 'COMMON.INTERACT'
319 real(kind=8),dimension(3) :: xx
320 real(kind=8) :: alphi,omegi,theta2
321 real(kind=8) :: dsci,dsci_inv,sinalphi,cosalphi,cosomegi,sinomegi
322 real(kind=8) :: xp,yp,zp,cost2,sint2,rj
324 ! dsci_inv=dsc_inv(itype(i))
326 dsci_inv=vbld_inv(i+nres)
333 call proc_proc(alphi,icrc)
334 if(icrc.eq.1)alphi=100.0
336 call proc_proc(omegi,icrc)
337 if(icrc.eq.1)omegi=-100.0
339 if (alphi.ne.alphi) alphi=100.0
340 if (omegi.ne.omegi) omegi=-100.0
351 yp= dsci*sinalphi*cosomegi
352 zp=-dsci*sinalphi*sinomegi
353 ! Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
354 ! X-axis aligned with the vector DC(*,i)
355 theta2=pi-0.5D0*theta(i+1)
358 xx(1)= xp*cost2+yp*sint2
359 xx(2)=-xp*sint2+yp*cost2
361 !d print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i)),i,
362 !d & xp,yp,zp,(xx(k),k=1,3)
366 ! Bring the SC vectors to the common coordinate system.
368 xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
369 xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
376 rj=rj+prod(j,k,i-1)*xx(k)
379 dc_norm(j,nres+i)=rj*dsci_inv
380 c(j,nres+i)=c(j,i)+rj
383 end subroutine locate_side_chain
384 !-----------------------------------------------------------------------------
386 !-----------------------------------------------------------------------------
387 subroutine int_from_cart1(lprn)
388 ! implicit real*8 (a-h,o-z)
389 ! include 'DIMENSIONS'
394 ! include 'COMMON.IOUNITS'
395 ! include 'COMMON.VAR'
396 ! include 'COMMON.CHAIN'
397 ! include 'COMMON.GEO'
398 ! include 'COMMON.INTERACT'
399 ! include 'COMMON.LOCAL'
400 ! include 'COMMON.NAMES'
401 ! include 'COMMON.SETUP'
402 ! include 'COMMON.TIME1'
406 real(kind=8) :: dnorm1,dnorm2,be
409 if (lprn) write (iout,'(/a)') 'Recalculated internal coordinates'
416 !write(iout,*)"geometry warring, vbld=",(vbld(i),i=1,nres+1)
418 vbld_inv(nres+1)=0.0d0
419 vbld_inv(2*nres)=0.0d0
422 #if defined(PARINT) && defined(MPI)
423 do i=iint_start,iint_end
430 c(j,nres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))/dnorm1 &
431 +(c(j,i+1)-c(j,i))/dnorm2)
435 if (i.le.nres) phi(i+1)=beta(i-2,i-1,i,i+1)
436 if ((itype(i).ne.10).and.(itype(i-1).ne.10)) then
437 tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
439 if (itype(i-1).ne.10) then
440 tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
441 omicron(1,i)=alpha(i-2,i-1,i-1+nres)
442 omicron(2,i)=alpha(i-1+nres,i-1,i)
444 if (itype(i).ne.10) then
445 tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
448 omeg(i)=beta(nres+i,i,nres2,i+1)
449 alph(i)=alpha(nres+i,i,nres2)
450 theta(i+1)=alpha(i-1,i,i+1)
452 vbld_inv(i)=1.0d0/vbld(i)
453 vbld(nres+i)=dist(nres+i,i)
454 if (itype(i).ne.10) then
455 vbld_inv(nres+i)=1.0d0/vbld(nres+i)
457 vbld_inv(nres+i)=0.0d0
460 #if defined(PARINT) && defined(MPI)
461 if (nfgtasks1.gt.1) then
462 !d write(iout,*) "iint_start",iint_start," iint_count",
463 !d & (iint_count(i),i=0,nfgtasks-1)," iint_displ",
464 !d & (iint_displ(i),i=0,nfgtasks-1)
465 !d write (iout,*) "Gather vbld backbone"
468 call MPI_Allgatherv(vbld(iint_start),iint_count(fg_rank1),&
469 MPI_DOUBLE_PRECISION,vbld(1),iint_count(0),iint_displ(0),&
470 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
471 !d write (iout,*) "Gather vbld_inv"
473 call MPI_Allgatherv(vbld_inv(iint_start),iint_count(fg_rank1),&
474 MPI_DOUBLE_PRECISION,vbld_inv(1),iint_count(0),iint_displ(0),&
475 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
476 !d write (iout,*) "Gather vbld side chain"
478 call MPI_Allgatherv(vbld(iint_start+nres),iint_count(fg_rank1),&
479 MPI_DOUBLE_PRECISION,vbld(nres+1),iint_count(0),iint_displ(0),&
480 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
481 !d write (iout,*) "Gather vbld_inv side chain"
483 call MPI_Allgatherv(vbld_inv(iint_start+nres),&
484 iint_count(fg_rank1),MPI_DOUBLE_PRECISION,vbld_inv(nres+1),&
485 iint_count(0),iint_displ(0),MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
486 !d write (iout,*) "Gather theta"
488 call MPI_Allgatherv(theta(iint_start+1),iint_count(fg_rank1),&
489 MPI_DOUBLE_PRECISION,theta(2),iint_count(0),iint_displ(0),&
490 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
491 !d write (iout,*) "Gather phi"
493 call MPI_Allgatherv(phi(iint_start+1),iint_count(fg_rank1),&
494 MPI_DOUBLE_PRECISION,phi(2),iint_count(0),iint_displ(0),&
495 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
497 !d write (iout,*) "Gather alph"
499 call MPI_Allgatherv(alph(iint_start),iint_count(fg_rank1),&
500 MPI_DOUBLE_PRECISION,alph(1),iint_count(0),iint_displ(0),&
501 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
502 !d write (iout,*) "Gather omeg"
504 call MPI_Allgatherv(omeg(iint_start),iint_count(fg_rank1),&
505 MPI_DOUBLE_PRECISION,omeg(1),iint_count(0),iint_displ(0),&
506 MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
508 time_gather=time_gather+MPI_Wtime()-time00
514 #if defined(WHAM_RUN) || defined(CLUSTER)
515 dc(j,i)=c(j,i+1)-c(j,i)
517 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
523 #if defined(WHAM_RUN) || defined(CLUSTER)
524 dc(j,i+nres)=c(j,i+nres)-c(j,i)
526 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
531 write (iout,1212) restyp(itype(i)),i,vbld(i),&
532 rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),&
533 rad2deg*alph(i),rad2deg*omeg(i)
536 1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
538 time_intfcart=time_intfcart+MPI_Wtime()-time01
541 end subroutine int_from_cart1
542 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
543 !-----------------------------------------------------------------------------
545 !-----------------------------------------------------------------------------
546 subroutine check_sc_distr
547 ! implicit real*8 (a-h,o-z)
548 ! include 'DIMENSIONS'
549 ! include 'COMMON.TIME1'
550 ! include 'COMMON.INTERACT'
551 ! include 'COMMON.NAMES'
552 ! include 'COMMON.GEO'
553 ! include 'COMMON.HEADER'
554 ! include 'COMMON.CONTROL'
556 real(kind=8),dimension(6*nres) :: varia !(maxvar) (maxvar=6*maxres)
557 real(kind=8) :: hrtime,mintime,sectime
558 integer,parameter :: MaxSample=10000000
559 real(kind=8),parameter :: delt=1.0D0/MaxSample
560 real(kind=8),dimension(0:72,0:90) :: prob
562 integer :: it,i,j,isample,indal,indom
563 real(kind=8) :: al,om,dV
564 dV=2.0D0*5.0D0*deg2rad*deg2rad
567 if (it.eq.10) goto 10
568 open (20,file=restyp(it)//'_distr.sdc',status='unknown')
569 call gen_side(it,90.0D0 * deg2rad,al,om,fail)
572 open (20,file=restyp(it)//'_distr1.sdc',status='unknown')
578 do isample=1,MaxSample
579 call gen_side(it,90.0D0 * deg2rad,al,om,fail)
581 indom=(rad2deg*om+180.0D0)/5
582 prob(indom,indal)=prob(indom,indal)+delt
586 write (20,'(2f10.3,1pd15.5)') 2*i+0.0D0,5*j-180.0D0,&
592 end subroutine check_sc_distr
594 !-----------------------------------------------------------------------------
596 !-----------------------------------------------------------------------------
597 subroutine geom_to_var(n,x)
599 ! Transfer the geometry parameters to the variable array.
600 ! The positions of variables are as follows:
601 ! 1. Virtual-bond torsional angles: 1 thru nres-3
602 ! 2. Virtual-bond valence angles: nres-2 thru 2*nres-5
603 ! 3. The polar angles alpha of local SC orientation: 2*nres-4 thru
605 ! 4. The torsional angles omega of SC orientation: 2*nres-4+nside+1
606 ! thru 2*nre-4+2*nside
608 ! implicit real*8 (a-h,o-z)
609 ! include 'DIMENSIONS'
610 ! include 'COMMON.VAR'
611 ! include 'COMMON.GEO'
612 ! include 'COMMON.CHAIN'
614 real(kind=8),dimension(n) :: x
615 !d print *,'nres',nres,' nphi',nphi,' ntheta',ntheta,' nvar',nvar
618 !d print *,i,i-3,phi(i)
620 if (n.eq.nphi) return
623 !d print *,i,i-2+nphi,theta(i)
625 if (n.eq.nphi+ntheta) return
627 if (ialph(i,1).gt.0) then
628 x(ialph(i,1))=alph(i)
629 x(ialph(i,1)+nside)=omeg(i)
630 !d print *,i,ialph(i,1),ialph(i,1)+nside,alph(i),omeg(i)
634 end subroutine geom_to_var
635 !-----------------------------------------------------------------------------
636 subroutine var_to_geom(n,x)
638 ! Update geometry parameters according to the variable array.
640 ! implicit real*8 (a-h,o-z)
641 ! include 'DIMENSIONS'
642 ! include 'COMMON.VAR'
643 ! include 'COMMON.CHAIN'
644 ! include 'COMMON.GEO'
645 ! include 'COMMON.IOUNITS'
647 real(kind=8),dimension(n) :: x
648 logical :: change !,reduce
655 if (n.gt.nphi+ntheta) then
658 alph(ii)=x(nphi+ntheta+i)
659 omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
660 !elwrite(iout,*) "alph",ii,alph
661 !elwrite(iout,*) "omeg",ii,omeg
666 !elwrite(iout,*) "phi",i,phi
668 if (n.eq.nphi) return
671 !elwrite(iout,*) "theta",i,theta
672 if (theta(i).eq.pi) theta(i)=0.99d0*pi
676 end subroutine var_to_geom
677 !-----------------------------------------------------------------------------
678 logical function convert_side(alphi,omegi)
680 real(kind=8) :: alphi,omegi
681 !el real(kind=8) :: pinorm
682 ! include 'COMMON.GEO'
684 ! Apply periodicity restrictions.
685 if (alphi.gt.pi) then
687 omegi=pinorm(omegi+pi)
691 end function convert_side
692 !-----------------------------------------------------------------------------
693 logical function reduce(x)
695 ! Apply periodic restrictions to variables.
697 ! implicit real*8 (a-h,o-z)
698 ! include 'DIMENSIONS'
699 ! include 'COMMON.VAR'
700 ! include 'COMMON.CHAIN'
701 ! include 'COMMON.GEO'
702 logical :: zm,zmiana !,convert_side
703 real(kind=8),dimension(nvar) :: x
707 x(i-3)=pinorm(x(i-3))
709 if (nvar.gt.nphi+ntheta) then
713 x(ii)=thetnorm(x(ii))
714 x(iii)=pinorm(x(iii))
715 ! Apply periodic restrictions.
716 zm=convert_side(x(ii),x(iii))
720 if (nvar.eq.nphi) return
724 x(ii)=dmod(x(ii),dwapi)
725 ! Apply periodic restrictions.
726 if (x(ii).gt.pi) then
729 if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
730 if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
733 x(ii)=dmod(pi-x(ii),dwapi)
734 x(ii+nside)=pinorm(-x(ii+nside))
735 zm=convert_side(x(ii),x(ii+nside))
737 else if (x(ii).lt.-pi) then
742 x(ii)=dmod(pi-x(ii),dwapi)
743 x(ii+nside)=pinorm(-pi-x(ii+nside))
744 zm=convert_side(x(ii),x(ii+nside))
746 else if (x(ii).lt.0.0d0) then
749 if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
750 if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
753 x(ii+nside)=pinorm(-x(ii+nside))
754 zm=convert_side(x(ii),x(ii+nside))
761 !-----------------------------------------------------------------------------
762 real(kind=8) function thetnorm(x)
763 ! This function puts x within [0,2Pi].
766 ! include 'COMMON.GEO'
768 if (xx.lt.0.0d0) xx=xx+dwapi
769 if (xx.gt.0.9999d0*pi) xx=0.9999d0*pi
772 end function thetnorm
773 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
774 !-----------------------------------------------------------------------------
775 subroutine var_to_geom_restr(n,xx)
777 ! Update geometry parameters according to the variable array.
779 ! implicit real*8 (a-h,o-z)
780 ! include 'DIMENSIONS'
781 ! include 'COMMON.VAR'
782 ! include 'COMMON.CHAIN'
783 ! include 'COMMON.GEO'
784 ! include 'COMMON.IOUNITS'
786 real(kind=8),dimension(6*nres) :: x,xx !(maxvar) (maxvar=6*maxres)
787 logical :: change !,reduce
793 alph(ii)=x(nphi+ntheta+i)
794 omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
801 if (theta(i).eq.pi) theta(i)=0.99d0*pi
805 end subroutine var_to_geom_restr
806 !-----------------------------------------------------------------------------
808 !-----------------------------------------------------------------------------
809 subroutine gen_rand_conf(nstart,*)
810 ! Generate random conformation or chain cut and regrowth.
812 ! implicit real*8 (a-h,o-z)
813 ! include 'DIMENSIONS'
814 ! include 'COMMON.CHAIN'
815 ! include 'COMMON.LOCAL'
816 ! include 'COMMON.VAR'
817 ! include 'COMMON.INTERACT'
818 ! include 'COMMON.IOUNITS'
819 ! include 'COMMON.MCM'
820 ! include 'COMMON.GEO'
821 ! include 'COMMON.CONTROL'
822 logical :: back,fail !overlap,
824 integer :: i,nstart,maxsi,nsi,maxnit,nit,niter
825 integer :: it1,it2,it,j
826 !d print *,' CG Processor',me,' maxgen=',maxgen
828 !d write (iout,*) 'Gen_Rand_conf: nstart=',nstart
829 if (nstart.lt.5) then
831 phi(4)=gen_phi(4,iabs(itype(2)),iabs(itype(3)))
832 ! write(iout,*)'phi(4)=',rad2deg*phi(4)
833 if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2)),pi,phi(4))
834 ! write(iout,*)'theta(3)=',rad2deg*theta(3)
838 do while (fail.and.nsi.le.maxsi)
839 call gen_side(it1,theta(3),alph(2),omeg(2),fail)
842 if (nsi.gt.maxsi) return 1
857 do while (i.le.nres .and. niter.lt.maxgen)
858 if (i.lt.nstart) then
860 write (iout,'(/80(1h*)/2a/80(1h*))') &
861 'Generation procedure went down to ',&
862 'chain beginning. Cannot continue...'
863 write (*,'(/80(1h*)/2a/80(1h*))') &
864 'Generation procedure went down to ',&
865 'chain beginning. Cannot continue...'
872 ! print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,
873 ! & ' nit=',nit,' niter=',niter,' maxgen=',maxgen
874 phi(i+1)=gen_phi(i+1,it1,it)
876 phi(i)=gen_phi(i+1,it2,it1)
877 ! print *,'phi(',i,')=',phi(i)
878 theta(i-1)=gen_theta(it2,phi(i-1),phi(i))
882 do while (fail.and.nsi.le.maxsi)
883 call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail)
886 if (nsi.gt.maxsi) return 1
888 call locate_next_res(i-1)
890 theta(i)=gen_theta(it1,phi(i),phi(i+1))
894 do while (fail.and.nsi.le.maxsi)
895 call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail)
898 if (nsi.gt.maxsi) return 1
900 call locate_next_res(i)
901 if (overlap(i-1)) then
902 if (nit.lt.maxnit) then
912 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
914 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
925 if (niter.ge.maxgen) then
926 write (iout,'(a,2i5)') &
927 'Too many trials in conformation generation',niter,maxgen
928 write (*,'(a,2i5)') &
929 'Too many trials in conformation generation',niter,maxgen
934 c(j,nres+nres)=c(j,nres)
937 end subroutine gen_rand_conf
938 !-----------------------------------------------------------------------------
939 logical function overlap(i)
940 ! implicit real*8 (a-h,o-z)
941 ! include 'DIMENSIONS'
942 ! include 'COMMON.CHAIN'
943 ! include 'COMMON.INTERACT'
944 ! include 'COMMON.FFIELD'
945 integer :: i,j,iti,itj,iteli,itelj,k
946 real(kind=8) :: redfac,rcomp
952 if (iti.gt.ntyp) return
953 ! Check for SC-SC overlaps.
954 !d print *,'nnt=',nnt,' nct=',nct
957 if (j.lt.i-1 .or. ipot.ne.4) then
958 rcomp=sigmaii(iti,itj)
963 if (dist(nres+i,nres+j).lt.redfac*rcomp) then
965 ! print *,'overlap, SC-SC: i=',i,' j=',j,
966 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
971 ! Check for overlaps between the added peptide group and the preceding
975 c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
979 !d print *,'overlap, p-Sc: i=',i,' j=',j,
980 !d & ' dist=',dist(nres+j,maxres2+1)
981 if (dist(nres+j,nres2+1).lt.4.0D0*redfac) then
986 ! Check for overlaps between the added side chain and the preceding peptide
990 c(k,nres2+1)=0.5D0*(c(k,j)+c(k,j+1))
992 !d print *,'overlap, SC-p: i=',i,' j=',j,
993 !d & ' dist=',dist(nres+i,maxres2+1)
994 if (dist(nres+i,nres2+1).lt.4.0D0*redfac) then
999 ! Check for p-p overlaps
1001 c(j,nres2+2)=0.5D0*(c(j,i)+c(j,i+1))
1006 c(k,nres2+2)=0.5D0*(c(k,j)+c(k,j+1))
1008 !d print *,'overlap, p-p: i=',i,' j=',j,
1009 !d & ' dist=',dist(maxres2+1,maxres2+2)
1010 if(iteli.ne.0.and.itelj.ne.0)then
1011 if (dist(nres2+1,nres2+2).lt.rpp(iteli,itelj)*redfac) then
1018 end function overlap
1019 !-----------------------------------------------------------------------------
1020 real(kind=8) function gen_phi(i,it1,it2)
1021 use random, only:ran_number
1022 ! implicit real*8 (a-h,o-z)
1023 ! include 'DIMENSIONS'
1024 ! include 'COMMON.GEO'
1025 ! include 'COMMON.BOUNDS'
1026 integer :: i,it1,it2
1027 ! gen_phi=ran_number(-pi,pi)
1028 ! 8/13/98 Generate phi using pre-defined boundaries
1029 gen_phi=ran_number(phibound(1,i),phibound(2,i))
1031 end function gen_phi
1032 !-----------------------------------------------------------------------------
1033 real(kind=8) function gen_theta(it,gama,gama1)
1034 use random,only:binorm
1035 ! implicit real*8 (a-h,o-z)
1036 ! include 'DIMENSIONS'
1037 ! include 'COMMON.LOCAL'
1038 ! include 'COMMON.GEO'
1039 real(kind=8),dimension(2) :: y,z
1040 real(kind=8) :: theta_max,theta_min,sig,ak
1043 real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1044 ! print *,'gen_theta: it=',it
1047 if (dabs(gama).gt.dwapi) then
1054 if (dabs(gama1).gt.dwapi) then
1061 thet_pred_mean=a0thet(it)
1063 thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1064 +bthet(k,it,1,1)*z(k)
1068 sig=sig*thet_pred_mean+polthet(j,it)
1070 sig=0.5D0/(sig*sig+sigc0(it))
1071 ak=dexp(gthet(1,it)- &
1072 0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1073 ! print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1074 ! print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1075 theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1076 if (theta_temp.lt.theta_min) theta_temp=theta_min
1077 if (theta_temp.gt.theta_max) theta_temp=theta_max
1078 gen_theta=theta_temp
1079 ! print '(a)','Exiting GENTHETA.'
1081 end function gen_theta
1082 !-----------------------------------------------------------------------------
1083 subroutine gen_side(it,the,al,om,fail)
1084 use random, only:ran_number,mult_norm1
1085 ! implicit real*8 (a-h,o-z)
1086 ! include 'DIMENSIONS'
1087 ! include 'COMMON.GEO'
1088 ! include 'COMMON.LOCAL'
1089 ! include 'COMMON.SETUP'
1090 ! include 'COMMON.IOUNITS'
1091 real(kind=8) :: MaxBoxLen=10.0D0
1092 real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1093 real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1094 real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1095 real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1096 real(kind=8),dimension(2) :: y,cm,eig
1097 real(kind=8),dimension(2,2) :: box
1098 real(kind=8),dimension(100) :: work
1099 real(kind=8) :: eig_limit=1.0D-8
1100 real(kind=8) :: Big=10.0D0
1101 logical :: lprint,fail,lcheck
1103 integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob
1104 real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1105 real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1106 real(kind=8) :: which_lobe
1110 if (the.eq.0.0D0 .or. the.eq.pi) then
1112 write (*,'(a,i4,a,i3,a,1pe14.5)') &
1113 'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1115 !d write (iout,'(a,i3,a,1pe14.5)')
1116 !d & 'Error in GenSide: it=',it,' theta=',the
1121 tant=dtan(the-pipol)
1123 allocate(z(3,nlobit))
1124 allocate(W1(nlobit))
1125 allocate(detAp(nlobit))
1126 allocate(sumW(0:nlobit))
1129 print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1130 write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1132 print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1133 write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1137 zz1=tant-censc(1,i,it)
1140 a(k,l)=gaussc(k,l,i,it)
1143 detApi=a(2,2)*a(3,3)-a(2,3)**2
1144 Ap_inv(2,2)=a(3,3)/detApi
1145 Ap_inv(2,3)=-a(2,3)/detApi
1146 Ap_inv(3,2)=Ap_inv(2,3)
1147 Ap_inv(3,3)=a(2,2)/detApi
1149 write (*,'(/a,i2/)') 'Cluster #',i
1150 write (*,'(3(1pe14.5),5x,1pe14.5)') &
1151 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1152 write (iout,'(/a,i2/)') 'Cluster #',i
1153 write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1154 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1159 W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1163 W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1164 ! if (lprint) write(*,'(a,3(1pe15.5)/)')
1165 ! & 'detAp, W1, anormi',detApi,W1i,anormi
1169 zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1173 detAp(i)=dsqrt(detApi)
1177 print *,'W1:',(w1(i),i=1,nlobit)
1178 print *,'detAp:',(detAp(i),i=1,nlobit)
1181 print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1183 write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1184 write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1187 write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1191 ! Writing the distribution just to check the procedure
1193 dV=deg2rad**2*10.0D0
1197 fac=fac+W1(i)/detAp(i)
1199 fac=1.0D0/(2.0D0*fac*pi)
1200 !d print *,it,'fac=',fac
1209 a(j-1,k-1)=gaussc(j,k,i,it)
1221 wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1224 wart=wart+W1(i)*dexp(-0.5D0*wykl)
1231 ! print *,'y',y(1),y(2),' fac=',fac
1233 write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1238 ! print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1242 ! Calculate the CM of the system
1245 W1(i)=W1(i)/detAp(i)
1249 sumW(i)=sumW(i-1)+W1(i)
1254 cm(1)=cm(1)+z(2,j)*W1(j)
1255 cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1257 cm(1)=cm(1)/sumW(nlobit)
1258 cm(2)=cm(2)/sumW(nlobit)
1259 if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1260 cm(2).gt.Big .or. cm(2).lt.-Big) then
1261 !d write (iout,'(a)')
1262 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1263 !d write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1265 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1266 !d write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1270 !d print *,'CM:',cm(1),cm(2)
1272 ! Find the largest search distance from CM
1278 a(j-1,k-1)=gaussc(j,k,i,it)
1282 call f02faf('N','U',2,a,3,eig,work,100,ifail)
1284 call djacob(2,3,10000,1.0d-10,a,vec,eig)
1288 print *,'*************** CG Processor',me
1289 print *,'CM:',cm(1),cm(2)
1290 write (iout,*) '*************** CG Processor',me
1291 write (iout,*) 'CM:',cm(1),cm(2)
1292 print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1293 write (iout,'(A,8f10.5)') &
1294 'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1297 if (eig(1).lt.eig_limit) then
1299 'From Mult_Norm: Eigenvalues of A are too small.'
1301 'From Mult_Norm: Eigenvalues of A are too small.'
1308 radius=radius+pinorm(z(j+1,i)-cm(j))**2
1310 radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1311 if (radius.gt.radmax) radmax=radius
1313 if (radmax.gt.pi) radmax=pi
1315 ! Determine the boundaries of the search rectangle.
1318 print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1319 print '(a,4(1pe14.4))','radmax: ',radmax
1321 box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1322 box(2,1)=dmin1(cm(1)+radmax,pi)
1323 box(1,2)=cm(2)-radmax
1324 box(2,2)=cm(2)+radmax
1327 print *,'CG Processor',me,' Array BOX:'
1329 print *,'Array BOX:'
1331 print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1332 print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1334 write (iout,*)'CG Processor',me,' Array BOX:'
1336 write (iout,*)'Array BOX:'
1338 write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1339 write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1341 if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1343 write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1344 write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1346 ! write (iout,'(a)') 'Bad sampling box.'
1351 which_lobe=ran_number(0.0D0,sumW(nlobit))
1352 ! print '(a,1pe14.4)','which_lobe=',which_lobe
1354 if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1357 ! print *,'ilob=',ilob,' nlob=',nlob(it)
1361 a(i-1,j-1)=gaussc(i,j,ilob,it)
1364 !d print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1365 call mult_norm1(3,2,a,cm,box,y,fail)
1369 !d print *,'al=',al,' om=',om
1372 end subroutine gen_side
1373 !-----------------------------------------------------------------------------
1374 subroutine overlap_sc(scfail)
1376 ! Internal and cartesian coordinates must be consistent as input,
1377 ! and will be up-to-date on return.
1378 ! At the end of this procedure, scfail is true if there are
1379 ! overlapping residues left, or false otherwise (success)
1381 ! implicit real*8 (a-h,o-z)
1382 ! include 'DIMENSIONS'
1383 ! include 'COMMON.CHAIN'
1384 ! include 'COMMON.INTERACT'
1385 ! include 'COMMON.FFIELD'
1386 ! include 'COMMON.VAR'
1387 ! include 'COMMON.SBRIDGE'
1388 ! include 'COMMON.IOUNITS'
1389 logical :: had_overlaps,fail,scfail
1390 integer,dimension(nres) :: ioverlap !(maxres)
1391 integer :: ioverlap_last,k,maxsi,i,iti,nsi
1394 had_overlaps=.false.
1395 call overlap_sc_list(ioverlap,ioverlap_last)
1396 if (ioverlap_last.gt.0) then
1397 write (iout,*) '#OVERLAPing residues ',ioverlap_last
1398 write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1404 if (ioverlap_last.eq.0) exit
1406 do ires=1,ioverlap_last
1412 do while (fail.and.nsi.le.maxsi)
1413 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
1421 call overlap_sc_list(ioverlap,ioverlap_last)
1422 ! write (iout,*) 'Overlaping residues ',ioverlap_last,
1423 ! & (ioverlap(j),j=1,ioverlap_last)
1426 if (k.le.1000.and.ioverlap_last.eq.0) then
1428 if (had_overlaps) then
1429 write (iout,*) '#OVERLAPing all corrected after ',k,&
1430 ' random generation'
1434 write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1435 write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1441 write (iout,'(a30,i5,a12,i4)') &
1442 '#OVERLAP FAIL in gen_side after',maxsi,&
1446 end subroutine overlap_sc
1447 !-----------------------------------------------------------------------------
1448 subroutine overlap_sc_list(ioverlap,ioverlap_last)
1450 ! implicit real*8 (a-h,o-z)
1451 ! include 'DIMENSIONS'
1452 ! include 'COMMON.GEO'
1453 ! include 'COMMON.LOCAL'
1454 ! include 'COMMON.IOUNITS'
1455 ! include 'COMMON.CHAIN'
1456 ! include 'COMMON.INTERACT'
1457 ! include 'COMMON.FFIELD'
1458 ! include 'COMMON.VAR'
1459 ! include 'COMMON.CALC'
1461 integer,dimension(nres) :: ioverlap !(maxres)
1462 integer :: ioverlap_last
1465 real(kind=8) :: redfac,sig !rrij,sigsq,
1466 integer :: itypi,itypj,itypi1
1467 real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1471 ! Check for SC-SC overlaps and mark residues
1472 ! print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1474 do i=iatsc_s,iatsc_e
1475 itypi=iabs(itype(i))
1476 itypi1=iabs(itype(i+1))
1480 dxi=dc_norm(1,nres+i)
1481 dyi=dc_norm(2,nres+i)
1482 dzi=dc_norm(3,nres+i)
1483 dsci_inv=dsc_inv(itypi)
1485 do iint=1,nint_gr(i)
1486 do j=istart(i,iint),iend(i,iint)
1488 itypj=iabs(itype(j))
1489 dscj_inv=dsc_inv(itypj)
1490 sig0ij=sigma(itypi,itypj)
1491 chi1=chi(itypi,itypj)
1492 chi2=chi(itypj,itypi)
1499 alf12=0.5D0*(alf1+alf2)
1501 rcomp=sigmaii(itypi,itypj)
1503 rcomp=sigma(itypi,itypj)
1505 ! print '(2(a3,2i3),a3,2f10.5)',
1506 ! & ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1511 dxj=dc_norm(1,nres+j)
1512 dyj=dc_norm(2,nres+j)
1513 dzj=dc_norm(3,nres+j)
1514 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1518 sig=sig0ij*dsqrt(sigsq)
1519 rij_shift=1.0D0/rij-sig+sig0ij
1521 !t if ( 1.0/rij .lt. redfac*rcomp .or.
1522 !t & rij_shift.le.0.0D0 ) then
1523 if ( rij_shift.le.0.0D0 ) then
1524 !d write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1525 !d & 'overlap SC-SC: i=',i,' j=',j,
1526 !d & ' dist=',dist(nres+i,nres+j),' rcomp=',
1527 !d & rcomp,1.0/rij,rij_shift
1528 ioverlap_last=ioverlap_last+1
1529 ioverlap(ioverlap_last)=i
1530 do k=1,ioverlap_last-1
1531 if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1533 ioverlap_last=ioverlap_last+1
1534 ioverlap(ioverlap_last)=j
1535 do k=1,ioverlap_last-1
1536 if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1543 end subroutine overlap_sc_list
1545 !-----------------------------------------------------------------------------
1546 ! energy_p_new_barrier.F
1547 !-----------------------------------------------------------------------------
1548 subroutine sc_angular
1549 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1550 ! om12. Called by ebp, egb, and egbv.
1553 ! include 'COMMON.CALC'
1554 ! include 'COMMON.IOUNITS'
1558 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1559 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1560 om12=dxi*dxj+dyi*dyj+dzi*dzj
1562 ! Calculate eps1(om12) and its derivative in om12
1563 faceps1=1.0D0-om12*chiom12
1564 faceps1_inv=1.0D0/faceps1
1565 eps1=dsqrt(faceps1_inv)
1566 ! Following variable is eps1*deps1/dom12
1567 eps1_om12=faceps1_inv*chiom12
1572 ! write (iout,*) "om12",om12," eps1",eps1
1573 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1578 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1579 sigsq=1.0D0-facsig*faceps1_inv
1580 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1581 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1582 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1588 ! write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1589 ! write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1591 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1594 chipom12=chip12*om12
1595 facp=1.0D0-om12*chipom12
1597 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1598 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1599 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1600 ! Following variable is the square root of eps2
1601 eps2rt=1.0D0-facp1*facp_inv
1602 ! Following three variables are the derivatives of the square root of eps
1603 ! in om1, om2, and om12.
1604 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1605 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1606 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1607 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1608 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1609 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1610 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1611 ! & " eps2rt_om12",eps2rt_om12
1612 ! Calculate whole angle-dependent part of epsilon and contributions
1613 ! to its derivatives
1615 end subroutine sc_angular
1616 !-----------------------------------------------------------------------------
1618 !-----------------------------------------------------------------------------
1619 subroutine int_bounds(total_ints,lower_bound,upper_bound)
1620 ! implicit real*8 (a-h,o-z)
1621 ! include 'DIMENSIONS'
1623 ! include 'COMMON.SETUP'
1624 integer :: total_ints,lower_bound,upper_bound,nint
1625 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1626 integer :: i,nexcess
1627 nint=total_ints/nfgtasks
1631 nexcess=total_ints-nint*nfgtasks
1633 int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1637 lower_bound=lower_bound+int4proc(i)
1639 upper_bound=lower_bound+int4proc(fg_rank)
1640 lower_bound=lower_bound+1
1642 end subroutine int_bounds
1643 !-----------------------------------------------------------------------------
1644 subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1645 ! implicit real*8 (a-h,o-z)
1646 ! include 'DIMENSIONS'
1648 ! include 'COMMON.SETUP'
1649 integer :: total_ints,lower_bound,upper_bound,nint
1650 integer :: nexcess,i
1651 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1652 nint=total_ints/nfgtasks1
1656 nexcess=total_ints-nint*nfgtasks1
1658 int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1662 lower_bound=lower_bound+int4proc(i)
1664 upper_bound=lower_bound+int4proc(fg_rank1)
1665 lower_bound=lower_bound+1
1667 end subroutine int_bounds1
1668 !-----------------------------------------------------------------------------
1670 !-----------------------------------------------------------------------------
1671 subroutine chainbuild_cart
1672 ! implicit real*8 (a-h,o-z)
1673 ! include 'DIMENSIONS'
1678 ! include 'COMMON.SETUP'
1679 ! include 'COMMON.CHAIN'
1680 ! include 'COMMON.LOCAL'
1681 ! include 'COMMON.TIME1'
1682 ! include 'COMMON.IOUNITS'
1683 integer :: j,i,ierror,ierr
1684 real(kind=8) :: time00,time01
1686 if (nfgtasks.gt.1) then
1687 ! write (iout,*) "BCAST in chainbuild_cart"
1689 ! Broadcast the order to build the chain and compute internal coordinates
1690 ! to the slaves. The slaves receive the order in ERGASTULUM.
1692 ! write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1694 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1695 ! & (dc(j,i+nres),j=1,3)
1698 call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1699 time_bcast7=time_bcast7+MPI_Wtime()-time00
1701 call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1703 ! write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1705 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1706 ! & (dc(j,i+nres),j=1,3)
1708 ! write (iout,*) "End BCAST in chainbuild_cart"
1710 time_bcast=time_bcast+MPI_Wtime()-time00
1711 time_bcastc=time_bcastc+MPI_Wtime()-time01
1719 c(j,i)=c(j,i-1)+dc(j,i-1)
1724 c(j,i+nres)=c(j,i)+dc(j,i+nres)
1727 ! write (iout,*) "CHAINBUILD_CART"
1729 call int_from_cart1(.false.)
1731 end subroutine chainbuild_cart
1732 !-----------------------------------------------------------------------------
1734 !-----------------------------------------------------------------------------
1735 real(kind=8) function alpha(i1,i2,i3)
1737 ! Calculates the planar angle between atoms (i1), (i2), and (i3).
1739 ! implicit real*8 (a-h,o-z)
1740 ! include 'DIMENSIONS'
1741 ! include 'COMMON.GEO'
1742 ! include 'COMMON.CHAIN'
1745 real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1752 vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1753 wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1754 scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1758 !-----------------------------------------------------------------------------
1759 real(kind=8) function beta(i1,i2,i3,i4)
1761 ! Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1763 ! implicit real*8 (a-h,o-z)
1764 ! include 'DIMENSIONS'
1765 ! include 'COMMON.GEO'
1766 ! include 'COMMON.CHAIN'
1768 integer :: i1,i2,i3,i4
1769 real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1770 real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1771 real(kind=8) :: tx,ty,tz
1781 !d print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1782 !d print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1783 !d print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1787 wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1791 vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1792 if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1793 scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1794 if (dabs(scalar).gt.1.0D0) &
1795 scalar=0.99999999999999D0*scalar/dabs(scalar)
1797 !d print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1802 ! if (angle.le.0.0D0) angle=pi+angle
1806 scalar=tx*x23+ty*y23+tz*z23
1807 if (scalar.lt.0.0D0) angle=-angle
1811 !-----------------------------------------------------------------------------
1812 real(kind=8) function dist(i1,i2)
1814 ! Calculates the distance between atoms (i1) and (i2).
1816 ! implicit real*8 (a-h,o-z)
1817 ! include 'DIMENSIONS'
1818 ! include 'COMMON.GEO'
1819 ! include 'COMMON.CHAIN'
1822 real(kind=8) :: x12,y12,z12
1826 dist=dsqrt(x12*x12+y12*y12+z12*z12)
1829 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1830 !-----------------------------------------------------------------------------
1832 !-----------------------------------------------------------------------------
1833 subroutine local_move_init(debug)
1837 ! implicit real*8 (a-h,o-z)
1838 ! include 'DIMENSIONS' ! Needed by COMMON.LOCAL
1839 ! include 'COMMON.GEO' ! For pi, deg2rad
1840 ! include 'COMMON.LOCAL' ! For vbl
1841 ! include 'COMMON.LOCMOVE'
1847 ! Determine wheter to do some debugging output
1848 locmove_output=debug
1850 ! Set the init_called flag to 1
1853 ! The following are never changed
1854 min_theta=60.D0*deg2rad ! (0,PI)
1855 max_theta=175.D0*deg2rad ! (0,PI)
1856 dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1857 dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1860 small2=0.5*small*small
1862 ! Not really necessary...
1868 end subroutine local_move_init
1869 !-----------------------------------------------------------------------------
1870 subroutine local_move(n_start, n_end, PHImin, PHImax)
1871 ! Perform a local move between residues m and n (inclusive)
1872 ! PHImin and PHImax [0,PI] determine the size of the move
1873 ! Works on whatever structure is in the variables theta and phi,
1874 ! sidechain variables are left untouched
1875 ! The final structure is NOT minimized, but both the cartesian
1876 ! variables c and the angles are up-to-date at the end (no further
1877 ! chainbuild is required)
1879 use random,only:ran_number
1881 ! implicit real*8 (a-h,o-z)
1882 ! include 'DIMENSIONS'
1883 ! include 'COMMON.GEO'
1884 ! include 'COMMON.CHAIN'
1885 ! include 'COMMON.VAR'
1886 ! include 'COMMON.MINIM'
1887 ! include 'COMMON.SBRIDGE'
1888 ! include 'COMMON.LOCMOVE'
1890 ! External functions
1891 !EL integer move_res
1892 !EL external move_res
1893 !EL double precision ran_number
1894 !EL external ran_number
1897 integer :: n_start, n_end ! First and last residues to move
1898 real(kind=8) :: PHImin, PHImax ! min/max angles [0,PI]
1902 real(kind=8) :: min,max
1906 ! Check if local_move_init was called. This assumes that it
1907 ! would not be 1 if not explicitely initialized
1908 if (init_called.ne.1) then
1909 write(6,*)' *** local_move_init not called!!!'
1913 ! Quick check for crazy range
1914 if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
1915 write(6,'(a,i3,a,i3)') &
1916 ' *** Cannot make local move between n_start = ',&
1917 n_start,' and n_end = ',n_end
1921 ! Take care of end residues first...
1922 if (n_start.eq.1) then
1923 ! Move residue 1 (completely random)
1924 theta(3)=ran_number(min_theta,max_theta)
1925 phi(4)=ran_number(-PI,PI)
1930 if (n_end.eq.nres) then
1931 ! Move residue nres (completely random)
1932 theta(nres)=ran_number(min_theta,max_theta)
1933 phi(nres)=ran_number(-PI,PI)
1939 ! ...then go through all other residues one by one
1940 ! Start from the two extremes and converge
1945 !$$$c Move the first two residues by less than the others
1946 !$$$ if (i-n_start.lt.3) then
1947 !$$$ if (i-n_start.eq.0) then
1950 !$$$ else if (i-n_start.eq.1) then
1953 !$$$ else if (i-n_start.eq.2) then
1959 ! The actual move, on residue i
1960 iretcode=move_res(min,max,i) ! Discard iretcode
1966 !$$$c Move the last two residues by less than the others
1967 !$$$ if (n_end-j.lt.3) then
1968 !$$$ if (n_end-j.eq.0) then
1971 !$$$ else if (n_end-j.eq.1) then
1974 !$$$ else if (n_end-j.eq.2) then
1980 ! The actual move, on residue j
1981 iretcode=move_res(min,max,j) ! Discard iretcode
1986 call int_from_cart(.false.,.false.)
1989 end subroutine local_move
1990 !-----------------------------------------------------------------------------
1991 subroutine output_tabs
1992 ! Prints out the contents of a_..., b_..., res_...
1996 ! include 'COMMON.GEO'
1997 ! include 'COMMON.LOCMOVE'
2003 write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2004 write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2007 write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2008 write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2011 write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2012 write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2013 write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2014 write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2017 end subroutine output_tabs
2018 !-----------------------------------------------------------------------------
2019 subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2020 ! Only uses angles if [0,PI] (but PHImin cannot be 0.,
2021 ! and PHImax cannot be PI)
2025 ! include 'COMMON.GEO'
2028 real(kind=8) :: PHImin,PHImax
2032 real(kind=8),dimension(0:3) :: ang
2033 logical,dimension(0:2,0:3) :: tab
2036 if (PHImin .eq. PHImax) then
2037 ! Special case with two 010's
2047 else if (PHImin .eq. PI) then
2048 ! Special case with one 010
2054 else if (PHImax .eq. 0.) then
2055 ! Special case with one 010
2064 if (PHImin .gt. 0.) then
2065 ! Start of range (011)
2070 ! End of range (110)
2074 tab(2,n+1) = .false.
2077 if (PHImax .lt. PI) then
2078 ! Start of range (011)
2083 ! End of range (110)
2087 tab(2,n+1) = .false.
2093 end subroutine angles2tab
2094 !-----------------------------------------------------------------------------
2095 subroutine minmax_angles(x,y,z,r,n,ang,tab)
2096 ! When solutions do not exist, assume all angles
2097 ! are acceptable - i.e., initial geometry must be correct
2101 ! include 'COMMON.GEO'
2102 ! include 'COMMON.LOCMOVE'
2105 real(kind=8) :: x,y,z,r
2109 real(kind=8),dimension(0:3) :: ang
2110 logical,dimension(0:2,0:3) :: tab
2113 real(kind=8) :: num, denom, phi
2114 real(kind=8) :: Kmin, Kmax
2118 num = x*x + y*y + z*z
2121 if (denom .gt. 0.) then
2123 denom = 2.*r*sqrt(denom)
2125 Kmin = (num - dmin2)/denom
2126 Kmax = (num - dmax2)/denom
2128 ! Allowed values of K (else all angles are acceptable)
2131 if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2133 else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2139 if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2141 else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2147 if (Kmax .lt. Kmin) Kmax = Kmin
2149 call angles2tab(Kmin, Kmax, n, ang, tab)
2151 ! Add phi and check that angles are within range (-PI,PI]
2154 if (ang(i) .le. -PI) then
2155 ang(i) = ang(i)+2.*PI
2156 else if (ang(i) .gt. PI) then
2157 ang(i) = ang(i)-2.*PI
2163 end subroutine minmax_angles
2164 !-----------------------------------------------------------------------------
2165 subroutine construct_tab
2166 ! Take a_... and b_... values and produces the results res_...
2167 ! x_ang are assumed to be all different (diff > small)
2168 ! x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2172 ! include 'COMMON.LOCMOVE'
2175 integer :: n_max,i,j,index
2181 if (n_max .eq. 0) then
2188 res_tab(j,0,i) = .true.
2189 res_tab(j,2,i) = .true.
2190 res_tab(j,1,i) = .false.
2197 do while (.not.done)
2198 res_ang(index) = flag
2202 if ((a_ang(i)-phi).gt.small .and. &
2203 a_ang(i) .lt. res_ang(index)) then
2204 ! Found a lower angle
2205 res_ang(index) = a_ang(i)
2206 ! Copy the values from a_tab into res_tab(0,,)
2207 res_tab(0,0,index) = a_tab(0,i)
2208 res_tab(0,1,index) = a_tab(1,i)
2209 res_tab(0,2,index) = a_tab(2,i)
2210 ! Set default values for res_tab(1,,)
2211 res_tab(1,0,index) = .true.
2212 res_tab(1,1,index) = .false.
2213 res_tab(1,2,index) = .true.
2214 else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2215 ! Found an equal angle (can only be equal to a b_ang)
2216 res_tab(0,0,index) = a_tab(0,i)
2217 res_tab(0,1,index) = a_tab(1,i)
2218 res_tab(0,2,index) = a_tab(2,i)
2223 if ((b_ang(i)-phi).gt.small .and. &
2224 b_ang(i) .lt. res_ang(index)) then
2225 ! Found a lower angle
2226 res_ang(index) = b_ang(i)
2227 ! Copy the values from b_tab into res_tab(1,,)
2228 res_tab(1,0,index) = b_tab(0,i)
2229 res_tab(1,1,index) = b_tab(1,i)
2230 res_tab(1,2,index) = b_tab(2,i)
2231 ! Set default values for res_tab(0,,)
2232 res_tab(0,0,index) = .true.
2233 res_tab(0,1,index) = .false.
2234 res_tab(0,2,index) = .true.
2235 else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2236 ! Found an equal angle (can only be equal to an a_ang)
2237 res_tab(1,0,index) = b_tab(0,i)
2238 res_tab(1,1,index) = b_tab(1,i)
2239 res_tab(1,2,index) = b_tab(2,i)
2243 if (res_ang(index) .eq. flag) then
2246 else if (index .eq. n_max-1) then
2250 phi = res_ang(index) ! Store previous angle
2258 if (a_n .gt. 0) then
2259 do while (.not.res_tab(0,1,index))
2262 done = res_tab(0,2,index)
2263 do i=index+1,res_n-1
2264 if (res_tab(0,1,i)) then
2265 done = res_tab(0,2,i)
2267 res_tab(0,0,i) = done
2268 res_tab(0,1,i) = done
2269 res_tab(0,2,i) = done
2272 done = res_tab(0,0,index)
2274 if (res_tab(0,1,i)) then
2275 done = res_tab(0,0,i)
2277 res_tab(0,0,i) = done
2278 res_tab(0,1,i) = done
2279 res_tab(0,2,i) = done
2284 res_tab(0,0,i) = .true.
2285 res_tab(0,1,i) = .true.
2286 res_tab(0,2,i) = .true.
2291 if (b_n .gt. 0) then
2292 do while (.not.res_tab(1,1,index))
2295 done = res_tab(1,2,index)
2296 do i=index+1,res_n-1
2297 if (res_tab(1,1,i)) then
2298 done = res_tab(1,2,i)
2300 res_tab(1,0,i) = done
2301 res_tab(1,1,i) = done
2302 res_tab(1,2,i) = done
2305 done = res_tab(1,0,index)
2307 if (res_tab(1,1,i)) then
2308 done = res_tab(1,0,i)
2310 res_tab(1,0,i) = done
2311 res_tab(1,1,i) = done
2312 res_tab(1,2,i) = done
2317 res_tab(1,0,i) = .true.
2318 res_tab(1,1,i) = .true.
2319 res_tab(1,2,i) = .true.
2323 ! Finally fill the last row with AND operation
2326 res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2331 end subroutine construct_tab
2332 !-----------------------------------------------------------------------------
2333 subroutine construct_ranges(phi_n,phi_start,phi_end)
2334 ! Given the data in res_..., construct a table of
2335 ! min/max allowed angles
2339 ! include 'COMMON.GEO'
2340 ! include 'COMMON.LOCMOVE'
2344 real(kind=8),dimension(0:11) :: phi_start,phi_end
2351 if (res_n .eq. 0) then
2352 ! Any move is allowed
2360 do while (.not.done)
2361 ! Find start of range (01x)
2363 do while (.not.done)
2364 if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2368 phi_start(phi_n) = res_ang(index)
2370 if (index .eq. res_n) done = .true.
2372 ! If a start was found (index < res_n), find the end of range (x10)
2373 ! It may not be found without wrapping around
2374 if (index .lt. res_n) then
2376 do while (.not.done)
2377 if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2382 if (index .eq. res_n) done = .true.
2384 if (index .lt. res_n) then
2385 ! Found the end of the range
2386 phi_end(phi_n) = res_ang(index)
2389 if (index .eq. res_n) then
2395 ! Need to wrap around
2397 phi_end(phi_n) = flag
2401 ! Take care of the last one if need to wrap around
2402 if (phi_end(phi_n) .eq. flag) then
2404 do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2407 phi_end(phi_n) = res_ang(index) + 2.*PI
2413 end subroutine construct_ranges
2414 !-----------------------------------------------------------------------------
2415 subroutine fix_no_moves(phi)
2419 ! include 'COMMON.GEO'
2420 ! include 'COMMON.LOCMOVE'
2427 real(kind=8) :: diff,temp
2430 ! Look for first 01x in gammas (there MUST be at least one)
2433 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2436 if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2437 ! Try to increase PHImax
2438 if (index .gt. 0) then
2439 phi = res_ang(index-1)
2440 diff = abs(res_ang(index) - res_ang(index-1))
2442 ! Look for last (corresponding) x10
2444 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2447 if (index .lt. res_n-1) then
2448 temp = abs(res_ang(index) - res_ang(index+1))
2449 if (temp .lt. diff) then
2450 phi = res_ang(index+1)
2456 ! If increasing PHImax didn't work, decreasing PHImin
2457 ! will (with one exception)
2458 ! Look for first x10 (there MUST be at least one)
2460 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2463 if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2464 ! Try to decrease PHImin
2465 if (index .lt. res_n-1) then
2466 temp = abs(res_ang(index) - res_ang(index+1))
2467 if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2468 phi = res_ang(index+1)
2472 ! Look for last (corresponding) 01x
2474 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2477 if (index .gt. 0) then
2478 temp = abs(res_ang(index) - res_ang(index-1))
2479 if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2480 phi = res_ang(index-1)
2486 ! If it still didn't work, it must be PHImax == 0. or PHImin == PI
2487 if (diff .eq. flag) then
2489 if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2490 res_tab(index,1,2)) index = res_n - 1
2491 ! This MUST work at this point
2492 if (index .eq. 0) then
2495 phi = res_ang(index - 1)
2500 end subroutine fix_no_moves
2501 !-----------------------------------------------------------------------------
2502 integer function move_res(PHImin,PHImax,i_move)
2503 ! Moves residue i_move (in array c), leaving everything else fixed
2504 ! Starting geometry is not checked, it should be correct!
2505 ! R(,i_move) is the only residue that will move, but must have
2506 ! 1 < i_move < nres (i.e., cannot move ends)
2507 ! Whether any output is done is controlled by locmove_output
2509 use random,only:ran_number
2511 ! implicit real*8 (a-h,o-z)
2512 ! include 'DIMENSIONS'
2513 ! include 'COMMON.CHAIN'
2514 ! include 'COMMON.GEO'
2515 ! include 'COMMON.LOCMOVE'
2517 ! External functions
2518 !EL double precision ran_number
2519 !EL external ran_number
2522 real(kind=8) :: PHImin,PHImax
2526 ! 0: move successfull
2527 ! 1: Dmin or Dmax had to be modified
2528 ! 2: move failed - check your input geometry
2532 real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2533 real(kind=8),dimension(0:2) :: P
2534 logical :: no_moves,done
2535 integer :: index,i,j
2536 real(kind=8) :: phi,temp,radius
2537 real(kind=8),dimension(0:11) :: phi_start,phi_end
2540 ! Set up the coordinate system
2542 Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2546 Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2548 temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2554 X(i)=c(i+1,i_move)-Orig(i)
2556 ! radius is the radius of the circle on which c(,i_move) can move
2557 radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2562 Y(0)=Z(1)*X(2)-X(1)*Z(2)
2563 Y(1)=X(0)*Z(2)-Z(0)*X(2)
2564 Y(2)=Z(0)*X(1)-X(0)*Z(1)
2566 ! Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2567 if (i_move.gt.2) then
2569 P(i)=c(i+1,i_move-2)-Orig(i)
2571 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2572 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2573 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2574 radius,a_n,a_ang,a_tab)
2579 ! Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2580 if (i_move.lt.nres-2) then
2582 P(i)=c(i+1,i_move+2)-Orig(i)
2584 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2585 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2586 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2587 radius,b_n,b_ang,b_tab)
2592 ! Construct the resulting table for alpha and beta
2593 call construct_tab()
2595 if (locmove_output) then
2596 print *,'ALPHAS & BETAS TABLE'
2600 ! Check that there is at least one possible move
2602 if (res_n .eq. 0) then
2606 do while ((index .lt. res_n) .and. no_moves)
2607 if (res_tab(2,1,index)) no_moves = .false.
2612 if (locmove_output) print *,' *** Cannot move anywhere'
2617 ! Transfer res_... into a_...
2620 if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2621 (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2622 a_ang(a_n) = res_ang(i)
2624 a_tab(j,a_n) = res_tab(2,j,i)
2630 ! Check that the PHI's are within [0,PI]
2631 if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2632 if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2633 if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2634 if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2635 if (PHImax .lt. PHImin) PHImax = PHImin
2636 ! Calculate min and max angles coming from PHImin and PHImax,
2637 ! and put them in b_...
2638 call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2639 ! Construct the final table
2640 call construct_tab()
2642 if (locmove_output) then
2643 print *,'FINAL TABLE'
2647 ! Check that there is at least one possible move
2649 if (res_n .eq. 0) then
2653 do while ((index .lt. res_n) .and. no_moves)
2654 if (res_tab(2,1,index)) no_moves = .false.
2660 ! Take care of the case where no solution exists...
2661 call fix_no_moves(phi)
2662 if (locmove_output) then
2663 print *,' *** Had to modify PHImin or PHImax'
2664 print *,'phi: ',phi*rad2deg
2668 ! ...or calculate the solution
2669 ! Construct phi_start/phi_end arrays
2670 call construct_ranges(phi_n, phi_start, phi_end)
2671 ! Choose random angle phi in allowed range(s)
2674 temp = temp + phi_end(i) - phi_start(i)
2676 phi = ran_number(phi_start(0),phi_start(0)+temp)
2679 do while (.not.done)
2680 if (phi .lt. phi_end(index)) then
2685 if (index .eq. phi_n) then
2687 else if (.not.done) then
2688 phi = phi + phi_start(index) - phi_end(index-1)
2691 if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2692 if (phi .gt. PI) phi = phi-2.*PI
2694 if (locmove_output) then
2695 print *,'ALLOWED RANGE(S)'
2697 print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2699 print *,'phi: ',phi*rad2deg
2704 ! Re-use radius as temp variable
2705 temp=radius*cos(phi)
2706 radius=radius*sin(phi)
2708 c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2712 end function move_res
2713 !-----------------------------------------------------------------------------
2718 ! implicit real*8 (a-h,o-z)
2719 ! include 'DIMENSIONS'
2720 ! include 'COMMON.GEO'
2721 ! include 'COMMON.LOCAL'
2722 ! include 'COMMON.LOCMOVE'
2724 ! External functions
2725 !EL integer move_res
2726 !EL external move_res
2731 real(kind=8),dimension(0:11) :: phi_start,phi_end
2733 real(kind=8),dimension(0:2,0:5) :: R
2735 locmove_output=.true.
2737 ! call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2738 ! call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2739 ! call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2740 ! call construct_tab
2743 ! call construct_ranges(phi_n,phi_start,phi_end)
2745 ! print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2748 ! call fix_no_moves(phi)
2749 ! print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2755 R(1,1)=-cos(28.D0*deg2rad)
2756 R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2760 R(0,3)=cos(30.D0*deg2rad)
2767 R(1,5)=cos(26.D0*deg2rad)
2768 R(2,5)=0.5D0+sin(26.D0*deg2rad)
2774 ! i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2776 i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2777 print *,'RETURNED ',i
2778 print *,(R(i,3)/vbl,i=0,2)
2781 end subroutine loc_test
2783 !-----------------------------------------------------------------------------
2785 !-----------------------------------------------------------------------------
2786 subroutine MATMULT(A1,A2,A3)
2787 ! implicit real*8 (a-h,o-z)
2788 ! include 'DIMENSIONS'
2791 real(kind=8) :: A3IJ
2793 real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2794 real(kind=8),DIMENSION(3,3) :: AI3
2799 3 A3IJ=A3IJ+A1(I,K)*A2(K,J)
2807 end subroutine MATMULT
2808 !-----------------------------------------------------------------------------
2810 !-----------------------------------------------------------------------------
2811 subroutine int_from_cart(lside,lprn)
2812 ! implicit real*8 (a-h,o-z)
2813 ! include 'DIMENSIONS'
2814 use control_data,only:out1file
2818 ! include 'COMMON.LOCAL'
2819 ! include 'COMMON.VAR'
2820 ! include 'COMMON.CHAIN'
2821 ! include 'COMMON.INTERACT'
2822 ! include 'COMMON.IOUNITS'
2823 ! include 'COMMON.GEO'
2824 ! include 'COMMON.NAMES'
2825 ! include 'COMMON.CONTROL'
2826 ! include 'COMMON.SETUP'
2827 character(len=3) :: seq,res
2829 character(len=80) :: card
2830 real(kind=8),dimension(3,20) :: sccor
2831 integer :: i,j,iti !el rescode,
2832 logical :: lside,lprn
2833 real(kind=8) :: di,cosfac,sinfac
2837 if(me.eq.king.or..not.out1file)then
2839 write (iout,'(/a)') &
2840 'Internal coordinates calculated from crystal structure.'
2842 write (iout,'(8a)') ' Res ',' dvb',' Theta',&
2843 ' Gamma',' Dsc_id',' Dsc',' Alpha',&
2846 write (iout,'(4a)') ' Res ',' dvb',' Theta',&
2852 !in wham do i=1,nres
2854 if (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0) then
2855 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2859 vbld(i+1)=dist(i,i+1)
2860 vbld_inv(i+1)=1.0d0/vbld(i+1)
2862 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2863 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2867 ! if (itype(1).eq.ntyp1) then
2869 ! c(j,1)=c(j,2)+(c(j,3)-c(j,4))
2872 ! if (itype(nres).eq.ntyp1) then
2874 ! c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
2878 ! if (unres_pdb) then
2879 ! if (itype(1).eq.21) then
2880 ! theta(3)=90.0d0*deg2rad
2881 ! phi(4)=180.0d0*deg2rad
2883 ! vbld_inv(2)=1.0d0/vbld(2)
2885 ! if (itype(nres).eq.21) then
2886 ! theta(nres)=90.0d0*deg2rad
2887 ! phi(nres)=180.0d0*deg2rad
2889 ! vbld_inv(nres)=1.0d0/vbld(2)
2895 c(j,nres2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
2896 +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
2897 ! in wham c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
2902 ! 10/03/12 Adam: Correction for zero SC-SC bond length
2903 if (itype(i).ne.10 .and. itype(i).ne.ntyp1 .and. di.eq.0.0d0) &
2906 if (itype(i).ne.10) then
2907 vbld_inv(i+nres)=1.0d0/di
2909 vbld_inv(i+nres)=0.0d0
2913 alph(i)=alpha(nres+i,i,nres2)
2914 omeg(i)=beta(nres+i,i,nres2,i+1)
2916 if(me.eq.king.or..not.out1file)then
2918 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,vbld(i),&
2919 rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
2920 rad2deg*alph(i),rad2deg*omeg(i)
2926 if(me.eq.king.or..not.out1file) &
2927 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),&
2928 rad2deg*theta(i),rad2deg*phi(i)
2932 end subroutine int_from_cart
2933 !-----------------------------------------------------------------------------
2934 subroutine sc_loc_geom(lprn)
2935 ! implicit real*8 (a-h,o-z)
2936 ! include 'DIMENSIONS'
2937 use control_data,only:out1file
2941 ! include 'COMMON.LOCAL'
2942 ! include 'COMMON.VAR'
2943 ! include 'COMMON.CHAIN'
2944 ! include 'COMMON.INTERACT'
2945 ! include 'COMMON.IOUNITS'
2946 ! include 'COMMON.GEO'
2947 ! include 'COMMON.NAMES'
2948 ! include 'COMMON.CONTROL'
2949 ! include 'COMMON.SETUP'
2950 real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
2953 integer :: i,j,it,iti
2954 real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
2957 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
2961 if (itype(i).ne.10) then
2963 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
2967 dc_norm(j,i+nres)=0.0d0
2972 costtab(i+1) =dcos(theta(i+1))
2973 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
2974 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
2975 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
2976 cosfac2=0.5d0/(1.0d0+costtab(i+1))
2977 cosfac=dsqrt(cosfac2)
2978 sinfac2=0.5d0/(1.0d0-costtab(i+1))
2979 sinfac=dsqrt(sinfac2)
2982 if ((it.ne.10).and.(it.ne.ntyp1)) then
2983 !el if (it.ne.10) then
2985 ! Compute the axes of tghe local cartesian coordinates system; store in
2986 ! x_prime, y_prime and z_prime
2994 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
2995 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
2997 call vecpr(x_prime,y_prime,z_prime)
2999 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3000 ! to local coordinate system. Store in xx, yy, zz.
3006 xx = xx + x_prime(j)*dc_norm(j,i+nres)
3007 yy = yy + y_prime(j)*dc_norm(j,i+nres)
3008 zz = zz + z_prime(j)*dc_norm(j,i+nres)
3023 if(me.eq.king.or..not.out1file) &
3024 write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),&
3030 end subroutine sc_loc_geom
3031 !-----------------------------------------------------------------------------
3032 subroutine sccenter(ires,nscat,sccor)
3033 ! implicit real*8 (a-h,o-z)
3034 ! include 'DIMENSIONS'
3035 ! include 'COMMON.CHAIN'
3036 integer :: i,j,ires,nscat
3037 real(kind=8),dimension(3,20) :: sccor
3038 real(kind=8) :: sccmj
3042 sccmj=sccmj+sccor(j,i)
3044 dc(j,ires)=sccmj/nscat
3047 end subroutine sccenter
3048 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3049 !-----------------------------------------------------------------------------
3050 subroutine bond_regular
3052 ! implicit real*8 (a-h,o-z)
3053 ! include 'DIMENSIONS'
3054 ! include 'COMMON.VAR'
3055 ! include 'COMMON.LOCAL'
3056 ! include 'COMMON.CALC'
3057 ! include 'COMMON.INTERACT'
3058 ! include 'COMMON.CHAIN'
3061 vbld_inv(i+1)=1.0d0/vbld(i+1)
3062 vbld(i+1+nres)=dsc(itype(i+1))
3063 vbld_inv(i+1+nres)=dsc_inv(itype(i+1))
3064 ! print *,vbld(i+1),vbld(i+1+nres)
3067 end subroutine bond_regular
3069 !-----------------------------------------------------------------------------
3071 !-----------------------------------------------------------------------------
3072 subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3073 ! This subroutine calculates unit vectors of a local reference system
3074 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3075 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3076 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3077 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3078 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3079 ! form a linear fragment. Returns vectors e1, e2, and e3.
3080 ! implicit real*8 (a-h,o-z)
3081 ! include 'DIMENSIONS'
3083 real(kind=8),dimension(3) :: e1,e2,e3
3084 real(kind=8),dimension(3) :: u,z
3085 ! include 'COMMON.IOUNITS'
3086 ! include 'COMMON.CHAIN'
3087 real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3089 integer :: i,i1,i2,i3,i4
3090 real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3103 if (s1.gt.coinc) goto 2
3104 write (iout,1000) i2,i3,i1
3109 2 if (s2.gt.coinc) goto 4
3110 write(iout,1000) i3,i4,i1
3117 v1=z(2)*u(3)-z(3)*u(2)
3118 v2=z(3)*u(1)-z(1)*u(3)
3119 v3=z(1)*u(2)-z(2)*u(1)
3120 anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3121 if (anorm.gt.align) goto 6
3122 write (iout,1010) i2,i3,i4,i1
3134 e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3135 e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3136 e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3137 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3138 'coordinates of atom',i4,' are set to zero.')
3139 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3140 ' fragment. coordinates of atom',i4,' are set to zero.')
3142 end subroutine refsys
3143 !-----------------------------------------------------------------------------
3145 !-----------------------------------------------------------------------------
3146 subroutine int_to_cart
3147 !--------------------------------------------------------------
3148 ! This subroutine converts the energy derivatives from internal
3149 ! coordinates to cartesian coordinates
3150 !-------------------------------------------------------------
3151 ! implicit real*8 (a-h,o-z)
3152 ! include 'DIMENSIONS'
3153 ! include 'COMMON.VAR'
3154 ! include 'COMMON.CHAIN'
3155 ! include 'COMMON.DERIV'
3156 ! include 'COMMON.GEO'
3157 ! include 'COMMON.LOCAL'
3158 ! include 'COMMON.INTERACT'
3159 ! include 'COMMON.MD'
3160 ! include 'COMMON.IOUNITS'
3161 ! include 'COMMON.SCCOR'
3162 ! calculating dE/ddc1
3165 if (nres.lt.3) go to 18
3167 gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3168 +gloc(nres-2,icg)*dtheta(j,1,3)
3169 if(itype(2).ne.10) then
3170 gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3171 gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3174 ! Calculating the remainder of dE/ddc2
3176 gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3177 gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3178 if(itype(2).ne.10) then
3179 gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3180 gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3182 if(itype(3).ne.10) then
3183 gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3184 gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3187 gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3190 ! If there are only five residues
3193 gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3194 dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3196 if(itype(3).ne.10) then
3197 gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3198 dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3200 if(itype(4).ne.10) then
3201 gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3202 dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3206 ! If there are more than five residues
3210 gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3211 +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3212 gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3213 gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3214 if(itype(i).ne.10) then
3215 gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3216 gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3218 if(itype(i+1).ne.10) then
3219 gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3220 +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3225 ! Setting dE/ddnres-2
3228 gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3229 dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3230 +gloc(2*nres-6,icg)* &
3231 dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3232 if(itype(nres-2).ne.10) then
3233 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3234 dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3237 if(itype(nres-1).ne.10) then
3238 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3239 dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3244 ! Settind dE/ddnres-1
3246 gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3247 gloc(2*nres-5,icg)*dtheta(j,2,nres)
3248 if(itype(nres-1).ne.10) then
3249 gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3250 dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3254 ! The side-chain vector derivatives
3256 if(itype(i).ne.10 .and. itype(i).ne.ntyp1) then
3258 gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3259 +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3263 !----------------------------------------------------------------------
3264 ! INTERTYP=1 SC...Ca...Ca...Ca
3265 ! INTERTYP=2 Ca...Ca...Ca...SC
3266 ! INTERTYP=3 SC...Ca...Ca...SC
3267 ! calculating dE/ddc1
3271 ! write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3273 if (nres.lt.2) return
3274 if ((nres.lt.3).and.(itype(1).eq.10)) return
3275 if ((itype(1).ne.10).and.(itype(1).ne.ntyp1)) then
3277 !c Derviative was calculated for oposite vector of side chain therefore
3278 ! there is "-" sign before gloc_sc
3279 gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3281 gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3283 if ((itype(2).ne.10).and.(itype(2).ne.ntyp1)) then
3284 gxcart(j,1)= gxcart(j,1) &
3285 -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3286 gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3291 if ((nres.ge.3).and.(itype(3).ne.10).and.(itype(3).ne.ntyp1)) &
3294 gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3297 ! As potetnial DO NOT depend on omicron anlge their derivative is
3299 ! & +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3301 ! Calculating the remainder of dE/ddc2
3303 if((itype(2).ne.10).and.(itype(2).ne.ntyp1)) then
3304 if (itype(1).ne.10) gxcart(j,2)=gxcart(j,2)+ &
3305 gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3306 if ((itype(3).ne.10).and.(nres.ge.3).and.(itype(3).ne.ntyp1)) &
3308 gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3309 !c the - above is due to different vector direction
3310 gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3313 gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3314 !c the - above is due to different vector direction
3315 gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3316 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3317 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3320 if ((itype(1).ne.10).and.(itype(1).ne.ntyp1)) then
3321 gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3322 ! write(iout,*) gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3324 if ((itype(3).ne.10).and.(nres.ge.3)) then
3325 gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3326 ! write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3328 if ((itype(4).ne.10).and.(nres.ge.4)) then
3329 gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3330 ! write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3333 ! write(iout,*) gcart(j,2),itype(2),itype(1),itype(3), "gcart2"
3335 ! If there are more than five residues
3339 ! write(iout,*) "before", gcart(j,i)
3340 if ((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then
3341 gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3342 *dtauangle(j,2,3,i+1) &
3343 -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3344 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3345 *dtauangle(j,1,2,i+2)
3346 ! write(iout,*) "new",j,i,
3347 ! & gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3348 if (itype(i-1).ne.10) then
3349 gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3350 *dtauangle(j,3,3,i+1)
3352 if (itype(i+1).ne.10) then
3353 gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3354 *dtauangle(j,3,1,i+2)
3355 gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3356 *dtauangle(j,3,2,i+2)
3359 if (itype(i-1).ne.10) then
3360 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3361 dtauangle(j,1,3,i+1)
3363 if (itype(i+1).ne.10) then
3364 gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3365 dtauangle(j,2,2,i+2)
3366 ! write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3367 ! & dtauangle(j,2,2,i+2)
3369 if (itype(i+2).ne.10) then
3370 gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3371 dtauangle(j,2,1,i+3)
3376 ! Setting dE/ddnres-1
3379 if ((itype(nres-1).ne.10).and.(itype(nres-1).ne.ntyp1)) then
3380 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3381 *dtauangle(j,2,3,nres)
3382 ! write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3383 ! & dtauangle(j,2,3,nres), gxcart(j,nres-1)
3384 if (itype(nres-2).ne.10) then
3385 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3386 *dtauangle(j,3,3,nres)
3388 if ((itype(nres).ne.10).and.(itype(nres).ne.ntyp1)) then
3389 gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3390 *dtauangle(j,3,1,nres+1)
3391 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3392 *dtauangle(j,3,2,nres+1)
3395 if ((itype(nres-2).ne.10).and.(itype(nres-2).ne.ntyp1)) then
3396 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3397 dtauangle(j,1,3,nres)
3399 if ((itype(nres).ne.10).and.(itype(nres).ne.ntyp1)) then
3400 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3401 dtauangle(j,2,2,nres+1)
3402 ! write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3403 ! & dtauangle(j,2,2,nres+1), itype(nres-1),itype(nres)
3408 if ((nres.ge.3).and.(itype(nres).ne.10).and. &
3409 (itype(nres).ne.ntyp1))then
3411 gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3412 *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3413 *dtauangle(j,2,3,nres+1)
3416 ! The side-chain vector derivatives
3418 end subroutine int_to_cart
3419 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3420 !-----------------------------------------------------------------------------
3422 !-----------------------------------------------------------------------------
3423 subroutine gen_dist_constr
3424 ! Generate CA distance constraints.
3425 ! implicit real*8 (a-h,o-z)
3426 ! include 'DIMENSIONS'
3427 ! include 'COMMON.IOUNITS'
3428 ! include 'COMMON.GEO'
3429 ! include 'COMMON.VAR'
3430 ! include 'COMMON.INTERACT'
3431 ! include 'COMMON.LOCAL'
3432 ! include 'COMMON.NAMES'
3433 ! include 'COMMON.CHAIN'
3434 ! include 'COMMON.FFIELD'
3435 ! include 'COMMON.SBRIDGE'
3436 ! include 'COMMON.HEADER'
3437 ! include 'COMMON.CONTROL'
3438 ! include 'COMMON.DBASE'
3439 ! include 'COMMON.THREAD'
3440 ! include 'COMMON.TIME1'
3441 ! integer :: itype_pdb !(maxres)
3442 ! common /pizda/ itype_pdb(nres)
3443 character(len=2) :: iden
3446 !d print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3447 !d write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3448 !d & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3450 do i=nstart_sup,nstart_sup+nsup-1
3451 !d write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3452 !d & ' seq_pdb', restyp(itype_pdb(i))
3453 do j=i+2,nstart_sup+nsup-1
3455 ihpb(nhpb)=i+nstart_seq-nstart_sup
3456 jhpb(nhpb)=j+nstart_seq-nstart_sup
3458 dhpb(nhpb)=dist(i,j)
3461 !d write (iout,'(a)') 'Distance constraints:'
3466 !d if (ii.gt.nres) then
3471 !d write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3472 !d & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3473 !d & dhpb(i),forcon(i)
3475 ! deallocate(itype_pdb)
3478 end subroutine gen_dist_constr
3480 !-----------------------------------------------------------------------------
3482 !-----------------------------------------------------------------------------
3483 subroutine cartprint
3485 use geometry_data, only: c
3486 use energy_data, only: itype
3487 ! implicit real*8 (a-h,o-z)
3488 ! include 'DIMENSIONS'
3489 ! include 'COMMON.CHAIN'
3490 ! include 'COMMON.INTERACT'
3491 ! include 'COMMON.NAMES'
3492 ! include 'COMMON.IOUNITS'
3497 write (iout,110) restyp(itype(i)),i,c(1,i),c(2,i),&
3498 c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3500 100 format (//' alpha-carbon coordinates ',&
3501 ' centroid coordinates'/ &
3502 ' ', 6X,'X',11X,'Y',11X,'Z',&
3503 10X,'X',11X,'Y',11X,'Z')
3504 110 format (a,'(',i3,')',6f12.5)
3506 end subroutine cartprint
3507 !-----------------------------------------------------------------------------
3508 !-----------------------------------------------------------------------------
3509 subroutine alloc_geo_arrays
3510 !EL Allocation of tables used by module energy
3512 integer :: i,j,nres2
3516 allocate(phibound(2,nres+2)) !(2,maxres)
3517 !----------------------
3519 ! common /chain/ in molread
3520 ! real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3521 ! real(kind=8),dimension(:,:),allocatable :: dc
3522 allocate(dc_old(3,0:nres2))
3523 ! if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3524 if(.not.allocated(dc_norm2)) then
3525 allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3533 !el if(.not.allocated(dc_norm))
3534 !elwrite(iout,*) "jestem w alloc geo 1"
3535 if(.not.allocated(dc_norm)) then
3536 allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3543 !elwrite(iout,*) "jestem w alloc geo 1"
3544 allocate(xloc(3,nres),xrot(3,nres))
3545 !elwrite(iout,*) "jestem w alloc geo 1"
3551 !elwrite(iout,*) "jestem w alloc geo 1"
3552 allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3554 allocate(t(3,3,nres),r(3,3,nres))
3555 allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3556 ! common /refstruct/
3557 if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3558 !elwrite(iout,*) "jestem w alloc geo 2"
3559 allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3560 if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3561 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3562 ! common /from_zscore/ in module.compare
3563 !----------------------
3565 ! Inverses of the actual virtual bond lengths
3566 ! common /invlen/ in io_conf: molread or readpdb
3567 ! real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3568 !----------------------
3570 ! Store the geometric variables in the following COMMON block.
3571 ! common /var/ in readpdb or ...
3572 if(.not.allocated(theta)) allocate(theta(nres+2))
3573 if(.not.allocated(phi)) allocate(phi(nres+2))
3574 if(.not.allocated(alph)) allocate(alph(nres+2))
3575 if(.not.allocated(omeg)) allocate(omeg(nres+2))
3576 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3577 if(.not.allocated(phiref)) allocate(phiref(nres+2))
3578 if(.not.allocated(costtab)) allocate(costtab(nres))
3579 if(.not.allocated(sinttab)) allocate(sinttab(nres))
3580 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3581 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3582 ! real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3583 allocate(omicron(2,nres+2)) !(2,maxres)
3584 allocate(tauangle(3,nres+2)) !(3,maxres)
3585 !elwrite(iout,*) "jestem w alloc geo 3"
3586 if(.not.allocated(xxtab)) allocate(xxtab(nres))
3587 if(.not.allocated(yytab)) allocate(yytab(nres))
3588 if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3589 if(.not.allocated(xxref)) allocate(xxref(nres))
3590 if(.not.allocated(yyref)) allocate(yyref(nres))
3591 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3592 allocate(ialph(nres,2)) !(maxres,2)
3595 allocate(ivar(4*nres2)) !(4*maxres2)
3597 #if defined(WHAM_RUN) || defined(CLUSTER)
3598 allocate(vbld(2*nres))
3602 allocate(vbld_inv(2*nres))
3609 end subroutine alloc_geo_arrays
3610 !-----------------------------------------------------------------------------
3611 !-----------------------------------------------------------------------------