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) goto 10
570 open (20,file=restyp(it,1)//'_distr.sdc',status='unknown')
571 call gen_side(it,90.0D0 * deg2rad,al,om,fail)
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)
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 ! implicit real*8 (a-h,o-z)
815 ! include 'DIMENSIONS'
816 ! include 'COMMON.CHAIN'
817 ! include 'COMMON.LOCAL'
818 ! include 'COMMON.VAR'
819 ! include 'COMMON.INTERACT'
820 ! include 'COMMON.IOUNITS'
821 ! include 'COMMON.MCM'
822 ! include 'COMMON.GEO'
823 ! include 'COMMON.CONTROL'
824 logical :: back,fail !overlap,
826 integer :: i,nstart,maxsi,nsi,maxnit,nit,niter
827 integer :: it1,it2,it,j
828 !d print *,' CG Processor',me,' maxgen=',maxgen
830 !d write (iout,*) 'Gen_Rand_conf: nstart=',nstart
831 if (nstart.lt.5) then
833 phi(4)=gen_phi(4,iabs(itype(2,1)),iabs(itype(3,1)))
834 ! write(iout,*)'phi(4)=',rad2deg*phi(4)
835 if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2,1)),pi,phi(4))
836 ! write(iout,*)'theta(3)=',rad2deg*theta(3)
840 do while (fail.and.nsi.le.maxsi)
841 call gen_side(it1,theta(3),alph(2),omeg(2),fail)
844 if (nsi.gt.maxsi) return 1
859 do while (i.le.nres .and. niter.lt.maxgen)
860 if (i.lt.nstart) then
862 write (iout,'(/80(1h*)/2a/80(1h*))') &
863 'Generation procedure went down to ',&
864 'chain beginning. Cannot continue...'
865 write (*,'(/80(1h*)/2a/80(1h*))') &
866 'Generation procedure went down to ',&
867 'chain beginning. Cannot continue...'
871 it1=iabs(itype(i-1,1))
872 it2=iabs(itype(i-2,1))
874 ! print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,
875 ! & ' nit=',nit,' niter=',niter,' maxgen=',maxgen
876 phi(i+1)=gen_phi(i+1,it1,it)
878 phi(i)=gen_phi(i+1,it2,it1)
879 ! print *,'phi(',i,')=',phi(i)
880 theta(i-1)=gen_theta(it2,phi(i-1),phi(i))
884 do while (fail.and.nsi.le.maxsi)
885 call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail)
888 if (nsi.gt.maxsi) return 1
890 call locate_next_res(i-1)
892 theta(i)=gen_theta(it1,phi(i),phi(i+1))
896 do while (fail.and.nsi.le.maxsi)
897 call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail)
900 if (nsi.gt.maxsi) return 1
902 call locate_next_res(i)
903 if (overlap(i-1)) then
904 if (nit.lt.maxnit) then
914 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
916 'Cannot generate non-overlaping conformation. Increase MAXNIT.'
927 if (niter.ge.maxgen) then
928 write (iout,'(a,2i5)') &
929 'Too many trials in conformation generation',niter,maxgen
930 write (*,'(a,2i5)') &
931 'Too many trials in conformation generation',niter,maxgen
936 c(j,nres+nres)=c(j,nres)
939 end subroutine gen_rand_conf
940 !-----------------------------------------------------------------------------
941 logical function overlap(i)
942 ! implicit real*8 (a-h,o-z)
943 ! include 'DIMENSIONS'
944 ! include 'COMMON.CHAIN'
945 ! include 'COMMON.INTERACT'
946 ! include 'COMMON.FFIELD'
947 integer :: i,j,iti,itj,iteli,itelj,k
948 real(kind=8) :: redfac,rcomp
954 if (iti.gt.ntyp) return
955 ! Check for SC-SC overlaps.
956 !d print *,'nnt=',nnt,' nct=',nct
959 if (j.lt.i-1 .or. ipot.ne.4) then
960 rcomp=sigmaii(iti,itj)
965 if (dist(nres+i,nres+j).lt.redfac*rcomp) then
967 ! print *,'overlap, SC-SC: i=',i,' j=',j,
968 ! & ' dist=',dist(nres+i,nres+j),' rcomp=',
973 ! Check for overlaps between the added peptide group and the preceding
977 ! c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
978 c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
982 !d print *,'overlap, p-Sc: i=',i,' j=',j,
983 !d & ' dist=',dist(nres+j,maxres2+1)
984 if (dist(nres+j,nres2+3).lt.4.0D0*redfac) then
989 ! Check for overlaps between the added side chain and the preceding peptide
993 c(k,nres2+3)=0.5D0*(c(k,j)+c(k,j+1))
995 !d print *,'overlap, SC-p: i=',i,' j=',j,
996 !d & ' dist=',dist(nres+i,maxres2+1)
997 if (dist(nres+i,nres2+3).lt.4.0D0*redfac) then
1002 ! Check for p-p overlaps
1004 c(j,nres2+4)=0.5D0*(c(j,i)+c(j,i+1))
1009 c(k,nres2+4)=0.5D0*(c(k,j)+c(k,j+1))
1011 !d print *,'overlap, p-p: i=',i,' j=',j,
1012 !d & ' dist=',dist(maxres2+1,maxres2+2)
1013 if(iteli.ne.0.and.itelj.ne.0)then
1014 if (dist(nres2+3,nres2+4).lt.rpp(iteli,itelj)*redfac) then
1021 end function overlap
1022 !-----------------------------------------------------------------------------
1023 real(kind=8) function gen_phi(i,it1,it2)
1024 use random, only:ran_number
1025 ! implicit real*8 (a-h,o-z)
1026 ! include 'DIMENSIONS'
1027 ! include 'COMMON.GEO'
1028 ! include 'COMMON.BOUNDS'
1029 integer :: i,it1,it2
1030 ! gen_phi=ran_number(-pi,pi)
1031 ! 8/13/98 Generate phi using pre-defined boundaries
1032 gen_phi=ran_number(phibound(1,i),phibound(2,i))
1034 end function gen_phi
1035 !-----------------------------------------------------------------------------
1036 real(kind=8) function gen_theta(it,gama,gama1)
1037 use random,only:binorm
1038 ! implicit real*8 (a-h,o-z)
1039 ! include 'DIMENSIONS'
1040 ! include 'COMMON.LOCAL'
1041 ! include 'COMMON.GEO'
1042 real(kind=8),dimension(2) :: y,z
1043 real(kind=8) :: theta_max,theta_min,sig,ak
1046 real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1047 ! print *,'gen_theta: it=',it
1050 if (dabs(gama).gt.dwapi) then
1057 if (dabs(gama1).gt.dwapi) then
1064 thet_pred_mean=a0thet(it)
1066 thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1067 +bthet(k,it,1,1)*z(k)
1071 sig=sig*thet_pred_mean+polthet(j,it)
1073 sig=0.5D0/(sig*sig+sigc0(it))
1074 ak=dexp(gthet(1,it)- &
1075 0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1076 ! print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1077 ! print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1078 theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1079 if (theta_temp.lt.theta_min) theta_temp=theta_min
1080 if (theta_temp.gt.theta_max) theta_temp=theta_max
1081 gen_theta=theta_temp
1082 ! print '(a)','Exiting GENTHETA.'
1084 end function gen_theta
1085 !-----------------------------------------------------------------------------
1086 subroutine gen_side(it,the,al,om,fail)
1087 use random, only:ran_number,mult_norm1
1088 ! implicit real*8 (a-h,o-z)
1089 ! include 'DIMENSIONS'
1090 ! include 'COMMON.GEO'
1091 ! include 'COMMON.LOCAL'
1092 ! include 'COMMON.SETUP'
1093 ! include 'COMMON.IOUNITS'
1094 real(kind=8) :: MaxBoxLen=10.0D0
1095 real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1096 real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1097 real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1098 real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1099 real(kind=8),dimension(2) :: y,cm,eig
1100 real(kind=8),dimension(2,2) :: box
1101 real(kind=8),dimension(100) :: work
1102 real(kind=8) :: eig_limit=1.0D-8
1103 real(kind=8) :: Big=10.0D0
1104 logical :: lprint,fail,lcheck
1106 integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob
1107 real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1108 real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1109 real(kind=8) :: which_lobe
1113 if (the.eq.0.0D0 .or. the.eq.pi) then
1115 write (*,'(a,i4,a,i3,a,1pe14.5)') &
1116 'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1118 !d write (iout,'(a,i3,a,1pe14.5)')
1119 !d & 'Error in GenSide: it=',it,' theta=',the
1124 tant=dtan(the-pipol)
1126 allocate(z(3,nlobit))
1127 allocate(W1(nlobit))
1128 allocate(detAp(nlobit))
1129 allocate(sumW(0:nlobit))
1132 print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1133 write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1135 print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1136 write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1140 zz1=tant-censc(1,i,it)
1143 a(k,l)=gaussc(k,l,i,it)
1146 detApi=a(2,2)*a(3,3)-a(2,3)**2
1147 Ap_inv(2,2)=a(3,3)/detApi
1148 Ap_inv(2,3)=-a(2,3)/detApi
1149 Ap_inv(3,2)=Ap_inv(2,3)
1150 Ap_inv(3,3)=a(2,2)/detApi
1152 write (*,'(/a,i2/)') 'Cluster #',i
1153 write (*,'(3(1pe14.5),5x,1pe14.5)') &
1154 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1155 write (iout,'(/a,i2/)') 'Cluster #',i
1156 write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1157 ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1162 W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1166 W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1167 ! if (lprint) write(*,'(a,3(1pe15.5)/)')
1168 ! & 'detAp, W1, anormi',detApi,W1i,anormi
1172 zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1176 detAp(i)=dsqrt(detApi)
1180 print *,'W1:',(w1(i),i=1,nlobit)
1181 print *,'detAp:',(detAp(i),i=1,nlobit)
1184 print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1186 write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1187 write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1190 write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1194 ! Writing the distribution just to check the procedure
1196 dV=deg2rad**2*10.0D0
1200 fac=fac+W1(i)/detAp(i)
1202 fac=1.0D0/(2.0D0*fac*pi)
1203 !d print *,it,'fac=',fac
1212 a(j-1,k-1)=gaussc(j,k,i,it)
1224 wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1227 wart=wart+W1(i)*dexp(-0.5D0*wykl)
1234 ! print *,'y',y(1),y(2),' fac=',fac
1236 write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1241 ! print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1245 ! Calculate the CM of the system
1248 W1(i)=W1(i)/detAp(i)
1252 sumW(i)=sumW(i-1)+W1(i)
1257 cm(1)=cm(1)+z(2,j)*W1(j)
1258 cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1260 cm(1)=cm(1)/sumW(nlobit)
1261 cm(2)=cm(2)/sumW(nlobit)
1262 if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1263 cm(2).gt.Big .or. cm(2).lt.-Big) then
1264 !d write (iout,'(a)')
1265 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1266 !d write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1268 !d & 'Unexpected error in GenSide - CM coordinates too large.'
1269 !d write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1273 !d print *,'CM:',cm(1),cm(2)
1275 ! Find the largest search distance from CM
1281 a(j-1,k-1)=gaussc(j,k,i,it)
1285 call f02faf('N','U',2,a,3,eig,work,100,ifail)
1287 call djacob(2,3,10000,1.0d-10,a,vec,eig)
1291 print *,'*************** CG Processor',me
1292 print *,'CM:',cm(1),cm(2)
1293 write (iout,*) '*************** CG Processor',me
1294 write (iout,*) 'CM:',cm(1),cm(2)
1295 print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1296 write (iout,'(A,8f10.5)') &
1297 'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1300 if (eig(1).lt.eig_limit) then
1302 'From Mult_Norm: Eigenvalues of A are too small.'
1304 'From Mult_Norm: Eigenvalues of A are too small.'
1311 radius=radius+pinorm(z(j+1,i)-cm(j))**2
1313 radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1314 if (radius.gt.radmax) radmax=radius
1316 if (radmax.gt.pi) radmax=pi
1318 ! Determine the boundaries of the search rectangle.
1321 print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1322 print '(a,4(1pe14.4))','radmax: ',radmax
1324 box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1325 box(2,1)=dmin1(cm(1)+radmax,pi)
1326 box(1,2)=cm(2)-radmax
1327 box(2,2)=cm(2)+radmax
1330 print *,'CG Processor',me,' Array BOX:'
1332 print *,'Array BOX:'
1334 print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1335 print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1337 write (iout,*)'CG Processor',me,' Array BOX:'
1339 write (iout,*)'Array BOX:'
1341 write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1342 write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1344 if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1346 write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1347 write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1349 ! write (iout,'(a)') 'Bad sampling box.'
1354 which_lobe=ran_number(0.0D0,sumW(nlobit))
1355 ! print '(a,1pe14.4)','which_lobe=',which_lobe
1357 if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1360 ! print *,'ilob=',ilob,' nlob=',nlob(it)
1364 a(i-1,j-1)=gaussc(i,j,ilob,it)
1367 !d print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1368 call mult_norm1(3,2,a,cm,box,y,fail)
1372 !d print *,'al=',al,' om=',om
1375 end subroutine gen_side
1376 !-----------------------------------------------------------------------------
1377 subroutine overlap_sc(scfail)
1379 ! Internal and cartesian coordinates must be consistent as input,
1380 ! and will be up-to-date on return.
1381 ! At the end of this procedure, scfail is true if there are
1382 ! overlapping residues left, or false otherwise (success)
1384 ! implicit real*8 (a-h,o-z)
1385 ! include 'DIMENSIONS'
1386 ! include 'COMMON.CHAIN'
1387 ! include 'COMMON.INTERACT'
1388 ! include 'COMMON.FFIELD'
1389 ! include 'COMMON.VAR'
1390 ! include 'COMMON.SBRIDGE'
1391 ! include 'COMMON.IOUNITS'
1392 logical :: had_overlaps,fail,scfail
1393 integer,dimension(nres) :: ioverlap !(maxres)
1394 integer :: ioverlap_last,k,maxsi,i,iti,nsi
1397 had_overlaps=.false.
1398 call overlap_sc_list(ioverlap,ioverlap_last)
1399 if (ioverlap_last.gt.0) then
1400 write (iout,*) '#OVERLAPing residues ',ioverlap_last
1401 write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1407 if (ioverlap_last.eq.0) exit
1409 do ires=1,ioverlap_last
1411 iti=iabs(itype(i,1))
1415 do while (fail.and.nsi.le.maxsi)
1416 call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
1424 call overlap_sc_list(ioverlap,ioverlap_last)
1425 ! write (iout,*) 'Overlaping residues ',ioverlap_last,
1426 ! & (ioverlap(j),j=1,ioverlap_last)
1429 if (k.le.1000.and.ioverlap_last.eq.0) then
1431 if (had_overlaps) then
1432 write (iout,*) '#OVERLAPing all corrected after ',k,&
1433 ' random generation'
1437 write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1438 write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1444 write (iout,'(a30,i5,a12,i4)') &
1445 '#OVERLAP FAIL in gen_side after',maxsi,&
1449 end subroutine overlap_sc
1450 !-----------------------------------------------------------------------------
1451 subroutine overlap_sc_list(ioverlap,ioverlap_last)
1453 ! implicit real*8 (a-h,o-z)
1454 ! include 'DIMENSIONS'
1455 ! include 'COMMON.GEO'
1456 ! include 'COMMON.LOCAL'
1457 ! include 'COMMON.IOUNITS'
1458 ! include 'COMMON.CHAIN'
1459 ! include 'COMMON.INTERACT'
1460 ! include 'COMMON.FFIELD'
1461 ! include 'COMMON.VAR'
1462 ! include 'COMMON.CALC'
1464 integer,dimension(nres) :: ioverlap !(maxres)
1465 integer :: ioverlap_last
1468 real(kind=8) :: redfac,sig !rrij,sigsq,
1469 integer :: itypi,itypj,itypi1
1470 real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1474 ! Check for SC-SC overlaps and mark residues
1475 ! print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1477 do i=iatsc_s,iatsc_e
1478 itypi=iabs(itype(i,1))
1479 itypi1=iabs(itype(i+1,1))
1483 dxi=dc_norm(1,nres+i)
1484 dyi=dc_norm(2,nres+i)
1485 dzi=dc_norm(3,nres+i)
1486 dsci_inv=dsc_inv(itypi)
1488 do iint=1,nint_gr(i)
1489 do j=istart(i,iint),iend(i,iint)
1491 itypj=iabs(itype(j,1))
1492 dscj_inv=dsc_inv(itypj)
1493 sig0ij=sigma(itypi,itypj)
1494 chi1=chi(itypi,itypj)
1495 chi2=chi(itypj,itypi)
1502 alf12=0.5D0*(alf1+alf2)
1504 rcomp=sigmaii(itypi,itypj)
1506 rcomp=sigma(itypi,itypj)
1508 ! print '(2(a3,2i3),a3,2f10.5)',
1509 ! & ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1514 dxj=dc_norm(1,nres+j)
1515 dyj=dc_norm(2,nres+j)
1516 dzj=dc_norm(3,nres+j)
1517 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1521 sig=sig0ij*dsqrt(sigsq)
1522 rij_shift=1.0D0/rij-sig+sig0ij
1524 !t if ( 1.0/rij .lt. redfac*rcomp .or.
1525 !t & rij_shift.le.0.0D0 ) then
1526 if ( rij_shift.le.0.0D0 ) then
1527 !d write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1528 !d & 'overlap SC-SC: i=',i,' j=',j,
1529 !d & ' dist=',dist(nres+i,nres+j),' rcomp=',
1530 !d & rcomp,1.0/rij,rij_shift
1531 ioverlap_last=ioverlap_last+1
1532 ioverlap(ioverlap_last)=i
1533 do k=1,ioverlap_last-1
1534 if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1536 ioverlap_last=ioverlap_last+1
1537 ioverlap(ioverlap_last)=j
1538 do k=1,ioverlap_last-1
1539 if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1546 end subroutine overlap_sc_list
1548 !-----------------------------------------------------------------------------
1549 ! energy_p_new_barrier.F
1550 !-----------------------------------------------------------------------------
1551 subroutine sc_angular
1552 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1553 ! om12. Called by ebp, egb, and egbv.
1556 ! include 'COMMON.CALC'
1557 ! include 'COMMON.IOUNITS'
1561 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1562 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1563 om12=dxi*dxj+dyi*dyj+dzi*dzj
1565 ! Calculate eps1(om12) and its derivative in om12
1566 faceps1=1.0D0-om12*chiom12
1567 faceps1_inv=1.0D0/faceps1
1568 eps1=dsqrt(faceps1_inv)
1569 ! Following variable is eps1*deps1/dom12
1570 eps1_om12=faceps1_inv*chiom12
1575 ! write (iout,*) "om12",om12," eps1",eps1
1576 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1581 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1582 sigsq=1.0D0-facsig*faceps1_inv
1583 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1584 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1585 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1591 ! write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1592 ! write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1594 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1597 chipom12=chip12*om12
1598 facp=1.0D0-om12*chipom12
1600 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1601 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1602 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1603 ! Following variable is the square root of eps2
1604 eps2rt=1.0D0-facp1*facp_inv
1605 ! Following three variables are the derivatives of the square root of eps
1606 ! in om1, om2, and om12.
1607 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1608 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1609 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1610 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1611 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1612 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1613 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1614 ! & " eps2rt_om12",eps2rt_om12
1615 ! Calculate whole angle-dependent part of epsilon and contributions
1616 ! to its derivatives
1618 end subroutine sc_angular
1619 !-----------------------------------------------------------------------------
1621 subroutine sc_angular_nucl
1622 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1623 ! om12. Called by ebp, egb, and egbv.
1626 ! include 'COMMON.CALC'
1627 ! include 'COMMON.IOUNITS'
1633 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1634 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1635 om12=dxi*dxj+dyi*dyj+dzi*dzj
1637 ! Calculate eps1(om12) and its derivative in om12
1638 faceps1=1.0D0-om12*chiom12
1639 faceps1_inv=1.0D0/faceps1
1640 eps1=dsqrt(faceps1_inv)
1641 ! Following variable is eps1*deps1/dom12
1642 eps1_om12=faceps1_inv*chiom12
1647 ! write (iout,*) "om12",om12," eps1",eps1
1648 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1653 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1654 sigsq=1.0D0-facsig*faceps1_inv
1655 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1656 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1657 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1660 chipom12=chip12*om12
1661 facp=1.0D0-om12*chipom12
1663 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1664 ! write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1665 ! & " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1666 ! Following variable is the square root of eps2
1667 eps2rt=1.0D0-facp1*facp_inv
1668 ! Following three variables are the derivatives of the square root of eps
1669 ! in om1, om2, and om12.
1670 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1671 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1672 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1673 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1674 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1675 ! write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1676 ! write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1677 ! & " eps2rt_om12",eps2rt_om12
1678 ! Calculate whole angle-dependent part of epsilon and contributions
1679 ! to its derivatives
1681 end subroutine sc_angular_nucl
1683 !-----------------------------------------------------------------------------
1684 subroutine int_bounds(total_ints,lower_bound,upper_bound)
1685 ! implicit real*8 (a-h,o-z)
1686 ! include 'DIMENSIONS'
1688 ! include 'COMMON.SETUP'
1689 integer :: total_ints,lower_bound,upper_bound,nint
1690 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1691 integer :: i,nexcess
1692 nint=total_ints/nfgtasks
1696 nexcess=total_ints-nint*nfgtasks
1698 int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1702 lower_bound=lower_bound+int4proc(i)
1704 upper_bound=lower_bound+int4proc(fg_rank)
1705 lower_bound=lower_bound+1
1707 end subroutine int_bounds
1708 !-----------------------------------------------------------------------------
1709 subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1710 ! implicit real*8 (a-h,o-z)
1711 ! include 'DIMENSIONS'
1713 ! include 'COMMON.SETUP'
1714 integer :: total_ints,lower_bound,upper_bound,nint
1715 integer :: nexcess,i
1716 integer,dimension(0:nfgtasks) :: int4proc,sint4proc !(0:max_fg_procs)
1717 nint=total_ints/nfgtasks1
1721 nexcess=total_ints-nint*nfgtasks1
1723 int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1727 lower_bound=lower_bound+int4proc(i)
1729 upper_bound=lower_bound+int4proc(fg_rank1)
1730 lower_bound=lower_bound+1
1732 end subroutine int_bounds1
1733 !-----------------------------------------------------------------------------
1735 !-----------------------------------------------------------------------------
1736 subroutine chainbuild_cart
1737 ! implicit real*8 (a-h,o-z)
1738 ! include 'DIMENSIONS'
1743 ! include 'COMMON.SETUP'
1744 ! include 'COMMON.CHAIN'
1745 ! include 'COMMON.LOCAL'
1746 ! include 'COMMON.TIME1'
1747 ! include 'COMMON.IOUNITS'
1748 integer :: j,i,ierror,ierr
1749 real(kind=8) :: time00,time01
1751 if (nfgtasks.gt.1) then
1752 ! write (iout,*) "BCAST in chainbuild_cart"
1754 ! Broadcast the order to build the chain and compute internal coordinates
1755 ! to the slaves. The slaves receive the order in ERGASTULUM.
1757 ! write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1759 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1760 ! & (dc(j,i+nres),j=1,3)
1763 call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1764 time_bcast7=time_bcast7+MPI_Wtime()-time00
1766 call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1768 ! write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1770 ! write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1771 ! & (dc(j,i+nres),j=1,3)
1773 ! write (iout,*) "End BCAST in chainbuild_cart"
1775 time_bcast=time_bcast+MPI_Wtime()-time00
1776 time_bcastc=time_bcastc+MPI_Wtime()-time01
1784 c(j,i)=c(j,i-1)+dc(j,i-1)
1789 c(j,i+nres)=c(j,i)+dc(j,i+nres)
1792 ! write (iout,*) "CHAINBUILD_CART"
1794 call int_from_cart1(.false.)
1796 end subroutine chainbuild_cart
1797 !-----------------------------------------------------------------------------
1799 !-----------------------------------------------------------------------------
1800 real(kind=8) function alpha(i1,i2,i3)
1802 ! Calculates the planar angle between atoms (i1), (i2), and (i3).
1804 ! implicit real*8 (a-h,o-z)
1805 ! include 'DIMENSIONS'
1806 ! include 'COMMON.GEO'
1807 ! include 'COMMON.CHAIN'
1810 real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1817 vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1818 wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1819 scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1823 !-----------------------------------------------------------------------------
1824 real(kind=8) function beta(i1,i2,i3,i4)
1826 ! Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1828 ! implicit real*8 (a-h,o-z)
1829 ! include 'DIMENSIONS'
1830 ! include 'COMMON.GEO'
1831 ! include 'COMMON.CHAIN'
1833 integer :: i1,i2,i3,i4
1834 real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1835 real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1836 real(kind=8) :: tx,ty,tz
1846 !d print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1847 !d print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1848 !d print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1852 wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1856 vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1857 if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1858 scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1859 if (dabs(scalar).gt.1.0D0) &
1860 scalar=0.99999999999999D0*scalar/dabs(scalar)
1862 !d print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1867 ! if (angle.le.0.0D0) angle=pi+angle
1871 scalar=tx*x23+ty*y23+tz*z23
1872 if (scalar.lt.0.0D0) angle=-angle
1876 !-----------------------------------------------------------------------------
1877 real(kind=8) function dist(i1,i2)
1879 ! Calculates the distance between atoms (i1) and (i2).
1881 ! implicit real*8 (a-h,o-z)
1882 ! include 'DIMENSIONS'
1883 ! include 'COMMON.GEO'
1884 ! include 'COMMON.CHAIN'
1887 real(kind=8) :: x12,y12,z12
1891 dist=dsqrt(x12*x12+y12*y12+z12*z12)
1894 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1895 !-----------------------------------------------------------------------------
1897 !-----------------------------------------------------------------------------
1898 subroutine local_move_init(debug)
1902 ! implicit real*8 (a-h,o-z)
1903 ! include 'DIMENSIONS' ! Needed by COMMON.LOCAL
1904 ! include 'COMMON.GEO' ! For pi, deg2rad
1905 ! include 'COMMON.LOCAL' ! For vbl
1906 ! include 'COMMON.LOCMOVE'
1912 ! Determine wheter to do some debugging output
1913 locmove_output=debug
1915 ! Set the init_called flag to 1
1918 ! The following are never changed
1919 min_theta=60.D0*deg2rad ! (0,PI)
1920 max_theta=175.D0*deg2rad ! (0,PI)
1921 dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1922 dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1925 small2=0.5*small*small
1927 ! Not really necessary...
1933 end subroutine local_move_init
1934 !-----------------------------------------------------------------------------
1935 subroutine local_move(n_start, n_end, PHImin, PHImax)
1936 ! Perform a local move between residues m and n (inclusive)
1937 ! PHImin and PHImax [0,PI] determine the size of the move
1938 ! Works on whatever structure is in the variables theta and phi,
1939 ! sidechain variables are left untouched
1940 ! The final structure is NOT minimized, but both the cartesian
1941 ! variables c and the angles are up-to-date at the end (no further
1942 ! chainbuild is required)
1944 use random,only:ran_number
1946 ! implicit real*8 (a-h,o-z)
1947 ! include 'DIMENSIONS'
1948 ! include 'COMMON.GEO'
1949 ! include 'COMMON.CHAIN'
1950 ! include 'COMMON.VAR'
1951 ! include 'COMMON.MINIM'
1952 ! include 'COMMON.SBRIDGE'
1953 ! include 'COMMON.LOCMOVE'
1955 ! External functions
1956 !EL integer move_res
1957 !EL external move_res
1958 !EL double precision ran_number
1959 !EL external ran_number
1962 integer :: n_start, n_end ! First and last residues to move
1963 real(kind=8) :: PHImin, PHImax ! min/max angles [0,PI]
1967 real(kind=8) :: min,max
1971 ! Check if local_move_init was called. This assumes that it
1972 ! would not be 1 if not explicitely initialized
1973 if (init_called.ne.1) then
1974 write(6,*)' *** local_move_init not called!!!'
1978 ! Quick check for crazy range
1979 if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
1980 write(6,'(a,i3,a,i3)') &
1981 ' *** Cannot make local move between n_start = ',&
1982 n_start,' and n_end = ',n_end
1986 ! Take care of end residues first...
1987 if (n_start.eq.1) then
1988 ! Move residue 1 (completely random)
1989 theta(3)=ran_number(min_theta,max_theta)
1990 phi(4)=ran_number(-PI,PI)
1995 if (n_end.eq.nres) then
1996 ! Move residue nres (completely random)
1997 theta(nres)=ran_number(min_theta,max_theta)
1998 phi(nres)=ran_number(-PI,PI)
2004 ! ...then go through all other residues one by one
2005 ! Start from the two extremes and converge
2010 !$$$c Move the first two residues by less than the others
2011 !$$$ if (i-n_start.lt.3) then
2012 !$$$ if (i-n_start.eq.0) then
2015 !$$$ else if (i-n_start.eq.1) then
2018 !$$$ else if (i-n_start.eq.2) then
2024 ! The actual move, on residue i
2025 iretcode=move_res(min,max,i) ! Discard iretcode
2031 !$$$c Move the last two residues by less than the others
2032 !$$$ if (n_end-j.lt.3) then
2033 !$$$ if (n_end-j.eq.0) then
2036 !$$$ else if (n_end-j.eq.1) then
2039 !$$$ else if (n_end-j.eq.2) then
2045 ! The actual move, on residue j
2046 iretcode=move_res(min,max,j) ! Discard iretcode
2051 call int_from_cart(.false.,.false.)
2054 end subroutine local_move
2055 !-----------------------------------------------------------------------------
2056 subroutine output_tabs
2057 ! Prints out the contents of a_..., b_..., res_...
2061 ! include 'COMMON.GEO'
2062 ! include 'COMMON.LOCMOVE'
2068 write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2069 write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2072 write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2073 write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2076 write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2077 write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2078 write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2079 write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2082 end subroutine output_tabs
2083 !-----------------------------------------------------------------------------
2084 subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2085 ! Only uses angles if [0,PI] (but PHImin cannot be 0.,
2086 ! and PHImax cannot be PI)
2090 ! include 'COMMON.GEO'
2093 real(kind=8) :: PHImin,PHImax
2097 real(kind=8),dimension(0:3) :: ang
2098 logical,dimension(0:2,0:3) :: tab
2101 if (PHImin .eq. PHImax) then
2102 ! Special case with two 010's
2112 else if (PHImin .eq. PI) then
2113 ! Special case with one 010
2119 else if (PHImax .eq. 0.) then
2120 ! Special case with one 010
2129 if (PHImin .gt. 0.) then
2130 ! Start of range (011)
2135 ! End of range (110)
2139 tab(2,n+1) = .false.
2142 if (PHImax .lt. PI) then
2143 ! Start of range (011)
2148 ! End of range (110)
2152 tab(2,n+1) = .false.
2158 end subroutine angles2tab
2159 !-----------------------------------------------------------------------------
2160 subroutine minmax_angles(x,y,z,r,n,ang,tab)
2161 ! When solutions do not exist, assume all angles
2162 ! are acceptable - i.e., initial geometry must be correct
2166 ! include 'COMMON.GEO'
2167 ! include 'COMMON.LOCMOVE'
2170 real(kind=8) :: x,y,z,r
2174 real(kind=8),dimension(0:3) :: ang
2175 logical,dimension(0:2,0:3) :: tab
2178 real(kind=8) :: num, denom, phi
2179 real(kind=8) :: Kmin, Kmax
2183 num = x*x + y*y + z*z
2186 if (denom .gt. 0.) then
2188 denom = 2.*r*sqrt(denom)
2190 Kmin = (num - dmin2)/denom
2191 Kmax = (num - dmax2)/denom
2193 ! Allowed values of K (else all angles are acceptable)
2196 if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2198 else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2204 if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2206 else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2212 if (Kmax .lt. Kmin) Kmax = Kmin
2214 call angles2tab(Kmin, Kmax, n, ang, tab)
2216 ! Add phi and check that angles are within range (-PI,PI]
2219 if (ang(i) .le. -PI) then
2220 ang(i) = ang(i)+2.*PI
2221 else if (ang(i) .gt. PI) then
2222 ang(i) = ang(i)-2.*PI
2228 end subroutine minmax_angles
2229 !-----------------------------------------------------------------------------
2230 subroutine construct_tab
2231 ! Take a_... and b_... values and produces the results res_...
2232 ! x_ang are assumed to be all different (diff > small)
2233 ! x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2237 ! include 'COMMON.LOCMOVE'
2240 integer :: n_max,i,j,index
2246 if (n_max .eq. 0) then
2253 res_tab(j,0,i) = .true.
2254 res_tab(j,2,i) = .true.
2255 res_tab(j,1,i) = .false.
2262 do while (.not.done)
2263 res_ang(index) = flag
2267 if ((a_ang(i)-phi).gt.small .and. &
2268 a_ang(i) .lt. res_ang(index)) then
2269 ! Found a lower angle
2270 res_ang(index) = a_ang(i)
2271 ! Copy the values from a_tab into res_tab(0,,)
2272 res_tab(0,0,index) = a_tab(0,i)
2273 res_tab(0,1,index) = a_tab(1,i)
2274 res_tab(0,2,index) = a_tab(2,i)
2275 ! Set default values for res_tab(1,,)
2276 res_tab(1,0,index) = .true.
2277 res_tab(1,1,index) = .false.
2278 res_tab(1,2,index) = .true.
2279 else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2280 ! Found an equal angle (can only be equal to a b_ang)
2281 res_tab(0,0,index) = a_tab(0,i)
2282 res_tab(0,1,index) = a_tab(1,i)
2283 res_tab(0,2,index) = a_tab(2,i)
2288 if ((b_ang(i)-phi).gt.small .and. &
2289 b_ang(i) .lt. res_ang(index)) then
2290 ! Found a lower angle
2291 res_ang(index) = b_ang(i)
2292 ! Copy the values from b_tab into res_tab(1,,)
2293 res_tab(1,0,index) = b_tab(0,i)
2294 res_tab(1,1,index) = b_tab(1,i)
2295 res_tab(1,2,index) = b_tab(2,i)
2296 ! Set default values for res_tab(0,,)
2297 res_tab(0,0,index) = .true.
2298 res_tab(0,1,index) = .false.
2299 res_tab(0,2,index) = .true.
2300 else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2301 ! Found an equal angle (can only be equal to an a_ang)
2302 res_tab(1,0,index) = b_tab(0,i)
2303 res_tab(1,1,index) = b_tab(1,i)
2304 res_tab(1,2,index) = b_tab(2,i)
2308 if (res_ang(index) .eq. flag) then
2311 else if (index .eq. n_max-1) then
2315 phi = res_ang(index) ! Store previous angle
2323 if (a_n .gt. 0) then
2324 do while (.not.res_tab(0,1,index))
2327 done = res_tab(0,2,index)
2328 do i=index+1,res_n-1
2329 if (res_tab(0,1,i)) then
2330 done = res_tab(0,2,i)
2332 res_tab(0,0,i) = done
2333 res_tab(0,1,i) = done
2334 res_tab(0,2,i) = done
2337 done = res_tab(0,0,index)
2339 if (res_tab(0,1,i)) then
2340 done = res_tab(0,0,i)
2342 res_tab(0,0,i) = done
2343 res_tab(0,1,i) = done
2344 res_tab(0,2,i) = done
2349 res_tab(0,0,i) = .true.
2350 res_tab(0,1,i) = .true.
2351 res_tab(0,2,i) = .true.
2356 if (b_n .gt. 0) then
2357 do while (.not.res_tab(1,1,index))
2360 done = res_tab(1,2,index)
2361 do i=index+1,res_n-1
2362 if (res_tab(1,1,i)) then
2363 done = res_tab(1,2,i)
2365 res_tab(1,0,i) = done
2366 res_tab(1,1,i) = done
2367 res_tab(1,2,i) = done
2370 done = res_tab(1,0,index)
2372 if (res_tab(1,1,i)) then
2373 done = res_tab(1,0,i)
2375 res_tab(1,0,i) = done
2376 res_tab(1,1,i) = done
2377 res_tab(1,2,i) = done
2382 res_tab(1,0,i) = .true.
2383 res_tab(1,1,i) = .true.
2384 res_tab(1,2,i) = .true.
2388 ! Finally fill the last row with AND operation
2391 res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2396 end subroutine construct_tab
2397 !-----------------------------------------------------------------------------
2398 subroutine construct_ranges(phi_n,phi_start,phi_end)
2399 ! Given the data in res_..., construct a table of
2400 ! min/max allowed angles
2404 ! include 'COMMON.GEO'
2405 ! include 'COMMON.LOCMOVE'
2409 real(kind=8),dimension(0:11) :: phi_start,phi_end
2416 if (res_n .eq. 0) then
2417 ! Any move is allowed
2425 do while (.not.done)
2426 ! Find start of range (01x)
2428 do while (.not.done)
2429 if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2433 phi_start(phi_n) = res_ang(index)
2435 if (index .eq. res_n) done = .true.
2437 ! If a start was found (index < res_n), find the end of range (x10)
2438 ! It may not be found without wrapping around
2439 if (index .lt. res_n) then
2441 do while (.not.done)
2442 if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2447 if (index .eq. res_n) done = .true.
2449 if (index .lt. res_n) then
2450 ! Found the end of the range
2451 phi_end(phi_n) = res_ang(index)
2454 if (index .eq. res_n) then
2460 ! Need to wrap around
2462 phi_end(phi_n) = flag
2466 ! Take care of the last one if need to wrap around
2467 if (phi_end(phi_n) .eq. flag) then
2469 do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2472 phi_end(phi_n) = res_ang(index) + 2.*PI
2478 end subroutine construct_ranges
2479 !-----------------------------------------------------------------------------
2480 subroutine fix_no_moves(phi)
2484 ! include 'COMMON.GEO'
2485 ! include 'COMMON.LOCMOVE'
2492 real(kind=8) :: diff,temp
2495 ! Look for first 01x in gammas (there MUST be at least one)
2498 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2501 if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2502 ! Try to increase PHImax
2503 if (index .gt. 0) then
2504 phi = res_ang(index-1)
2505 diff = abs(res_ang(index) - res_ang(index-1))
2507 ! Look for last (corresponding) x10
2509 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2512 if (index .lt. res_n-1) then
2513 temp = abs(res_ang(index) - res_ang(index+1))
2514 if (temp .lt. diff) then
2515 phi = res_ang(index+1)
2521 ! If increasing PHImax didn't work, decreasing PHImin
2522 ! will (with one exception)
2523 ! Look for first x10 (there MUST be at least one)
2525 do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2528 if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2529 ! Try to decrease PHImin
2530 if (index .lt. res_n-1) then
2531 temp = abs(res_ang(index) - res_ang(index+1))
2532 if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2533 phi = res_ang(index+1)
2537 ! Look for last (corresponding) 01x
2539 do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2542 if (index .gt. 0) then
2543 temp = abs(res_ang(index) - res_ang(index-1))
2544 if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2545 phi = res_ang(index-1)
2551 ! If it still didn't work, it must be PHImax == 0. or PHImin == PI
2552 if (diff .eq. flag) then
2554 if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2555 res_tab(index,1,2)) index = res_n - 1
2556 ! This MUST work at this point
2557 if (index .eq. 0) then
2560 phi = res_ang(index - 1)
2565 end subroutine fix_no_moves
2566 !-----------------------------------------------------------------------------
2567 integer function move_res(PHImin,PHImax,i_move)
2568 ! Moves residue i_move (in array c), leaving everything else fixed
2569 ! Starting geometry is not checked, it should be correct!
2570 ! R(,i_move) is the only residue that will move, but must have
2571 ! 1 < i_move < nres (i.e., cannot move ends)
2572 ! Whether any output is done is controlled by locmove_output
2574 use random,only:ran_number
2576 ! implicit real*8 (a-h,o-z)
2577 ! include 'DIMENSIONS'
2578 ! include 'COMMON.CHAIN'
2579 ! include 'COMMON.GEO'
2580 ! include 'COMMON.LOCMOVE'
2582 ! External functions
2583 !EL double precision ran_number
2584 !EL external ran_number
2587 real(kind=8) :: PHImin,PHImax
2591 ! 0: move successfull
2592 ! 1: Dmin or Dmax had to be modified
2593 ! 2: move failed - check your input geometry
2597 real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2598 real(kind=8),dimension(0:2) :: P
2599 logical :: no_moves,done
2600 integer :: index,i,j
2601 real(kind=8) :: phi,temp,radius
2602 real(kind=8),dimension(0:11) :: phi_start,phi_end
2605 ! Set up the coordinate system
2607 Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2611 Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2613 temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2619 X(i)=c(i+1,i_move)-Orig(i)
2621 ! radius is the radius of the circle on which c(,i_move) can move
2622 radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2627 Y(0)=Z(1)*X(2)-X(1)*Z(2)
2628 Y(1)=X(0)*Z(2)-Z(0)*X(2)
2629 Y(2)=Z(0)*X(1)-X(0)*Z(1)
2631 ! Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2632 if (i_move.gt.2) then
2634 P(i)=c(i+1,i_move-2)-Orig(i)
2636 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2637 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2638 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2639 radius,a_n,a_ang,a_tab)
2644 ! Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2645 if (i_move.lt.nres-2) then
2647 P(i)=c(i+1,i_move+2)-Orig(i)
2649 call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2650 P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2651 P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2652 radius,b_n,b_ang,b_tab)
2657 ! Construct the resulting table for alpha and beta
2658 call construct_tab()
2660 if (locmove_output) then
2661 print *,'ALPHAS & BETAS TABLE'
2665 ! Check that there is at least one possible move
2667 if (res_n .eq. 0) then
2671 do while ((index .lt. res_n) .and. no_moves)
2672 if (res_tab(2,1,index)) no_moves = .false.
2677 if (locmove_output) print *,' *** Cannot move anywhere'
2682 ! Transfer res_... into a_...
2685 if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2686 (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2687 a_ang(a_n) = res_ang(i)
2689 a_tab(j,a_n) = res_tab(2,j,i)
2695 ! Check that the PHI's are within [0,PI]
2696 if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2697 if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2698 if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2699 if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2700 if (PHImax .lt. PHImin) PHImax = PHImin
2701 ! Calculate min and max angles coming from PHImin and PHImax,
2702 ! and put them in b_...
2703 call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2704 ! Construct the final table
2705 call construct_tab()
2707 if (locmove_output) then
2708 print *,'FINAL TABLE'
2712 ! Check that there is at least one possible move
2714 if (res_n .eq. 0) then
2718 do while ((index .lt. res_n) .and. no_moves)
2719 if (res_tab(2,1,index)) no_moves = .false.
2725 ! Take care of the case where no solution exists...
2726 call fix_no_moves(phi)
2727 if (locmove_output) then
2728 print *,' *** Had to modify PHImin or PHImax'
2729 print *,'phi: ',phi*rad2deg
2733 ! ...or calculate the solution
2734 ! Construct phi_start/phi_end arrays
2735 call construct_ranges(phi_n, phi_start, phi_end)
2736 ! Choose random angle phi in allowed range(s)
2739 temp = temp + phi_end(i) - phi_start(i)
2741 phi = ran_number(phi_start(0),phi_start(0)+temp)
2744 do while (.not.done)
2745 if (phi .lt. phi_end(index)) then
2750 if (index .eq. phi_n) then
2752 else if (.not.done) then
2753 phi = phi + phi_start(index) - phi_end(index-1)
2756 if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2757 if (phi .gt. PI) phi = phi-2.*PI
2759 if (locmove_output) then
2760 print *,'ALLOWED RANGE(S)'
2762 print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2764 print *,'phi: ',phi*rad2deg
2769 ! Re-use radius as temp variable
2770 temp=radius*cos(phi)
2771 radius=radius*sin(phi)
2773 c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2777 end function move_res
2778 !-----------------------------------------------------------------------------
2783 ! implicit real*8 (a-h,o-z)
2784 ! include 'DIMENSIONS'
2785 ! include 'COMMON.GEO'
2786 ! include 'COMMON.LOCAL'
2787 ! include 'COMMON.LOCMOVE'
2789 ! External functions
2790 !EL integer move_res
2791 !EL external move_res
2796 real(kind=8),dimension(0:11) :: phi_start,phi_end
2798 real(kind=8),dimension(0:2,0:5) :: R
2800 locmove_output=.true.
2802 ! call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2803 ! call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2804 ! call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2805 ! call construct_tab
2808 ! call construct_ranges(phi_n,phi_start,phi_end)
2810 ! print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2813 ! call fix_no_moves(phi)
2814 ! print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2820 R(1,1)=-cos(28.D0*deg2rad)
2821 R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2825 R(0,3)=cos(30.D0*deg2rad)
2832 R(1,5)=cos(26.D0*deg2rad)
2833 R(2,5)=0.5D0+sin(26.D0*deg2rad)
2839 ! i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2841 i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2842 print *,'RETURNED ',i
2843 print *,(R(i,3)/vbl,i=0,2)
2846 end subroutine loc_test
2848 !-----------------------------------------------------------------------------
2850 !-----------------------------------------------------------------------------
2851 subroutine MATMULT(A1,A2,A3)
2852 ! implicit real*8 (a-h,o-z)
2853 ! include 'DIMENSIONS'
2856 real(kind=8) :: A3IJ
2858 real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2859 real(kind=8),DIMENSION(3,3) :: AI3
2864 3 A3IJ=A3IJ+A1(I,K)*A2(K,J)
2872 end subroutine MATMULT
2873 !-----------------------------------------------------------------------------
2875 !-----------------------------------------------------------------------------
2876 subroutine int_from_cart(lside,lprn)
2877 ! implicit real*8 (a-h,o-z)
2878 ! include 'DIMENSIONS'
2879 use control_data,only:out1file
2883 ! include 'COMMON.LOCAL'
2884 ! include 'COMMON.VAR'
2885 ! include 'COMMON.CHAIN'
2886 ! include 'COMMON.INTERACT'
2887 ! include 'COMMON.IOUNITS'
2888 ! include 'COMMON.GEO'
2889 ! include 'COMMON.NAMES'
2890 ! include 'COMMON.CONTROL'
2891 ! include 'COMMON.SETUP'
2892 character(len=3) :: seq,res
2894 character(len=80) :: card
2895 real(kind=8),dimension(3,20) :: sccor
2896 integer :: i,j,iti !el rescode,
2897 logical :: lside,lprn
2898 real(kind=8) :: di,cosfac,sinfac
2902 if(me.eq.king.or..not.out1file)then
2904 write (iout,'(/a)') &
2905 'Internal coordinates calculated from crystal structure.'
2907 write (iout,'(8a)') ' Res ',' dvb',' Theta',&
2908 ' Gamma',' Dsc_id',' Dsc',' Alpha',&
2911 write (iout,'(4a)') ' Res ',' dvb',' Theta',&
2917 ! if (molnum(i).ne.1) cycle
2918 !in wham do i=1,nres
2920 if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2921 (iti.ne.ntyp1 .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2922 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2926 vbld(i+1)=dist(i,i+1)
2927 vbld_inv(i+1)=1.0d0/vbld(i+1)
2929 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2930 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2934 ! if (itype(1,1).eq.ntyp1) then
2936 ! c(j,1)=c(j,2)+(c(j,3)-c(j,4))
2939 ! if (itype(nres,1).eq.ntyp1) then
2941 ! c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
2945 ! if (unres_pdb) then
2946 ! if (itype(1,1).eq.21) then
2947 ! theta(3)=90.0d0*deg2rad
2948 ! phi(4)=180.0d0*deg2rad
2950 ! vbld_inv(2)=1.0d0/vbld(2)
2952 ! if (itype(nres,1).eq.21) then
2953 ! theta(nres)=90.0d0*deg2rad
2954 ! phi(nres)=180.0d0*deg2rad
2956 ! vbld_inv(nres)=1.0d0/vbld(2)
2962 c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
2963 +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
2964 ! in wham c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
2969 ! 10/03/12 Adam: Correction for zero SC-SC bond length
2971 if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
2972 di=dsc(itype(i,molnum(i)))
2974 if (itype(i,1).ne.10) then
2975 vbld_inv(i+nres)=1.0d0/di
2977 vbld_inv(i+nres)=0.0d0
2981 alph(i)=alpha(nres+i,i,nres2+2)
2982 omeg(i)=beta(nres+i,i,nres2+2,i+1)
2985 if(me.eq.king.or..not.out1file)then
2987 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
2988 rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
2989 rad2deg*alph(i),rad2deg*omeg(i)
2992 if(me.eq.king.or..not.out1file)then
2994 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
2995 rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
2996 rad2deg*alph(i),rad2deg*omeg(i)
3003 if(me.eq.king.or..not.out1file) &
3004 write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3005 rad2deg*theta(i),rad2deg*phi(i)
3009 end subroutine int_from_cart
3010 !-----------------------------------------------------------------------------
3011 subroutine sc_loc_geom(lprn)
3012 ! implicit real*8 (a-h,o-z)
3013 ! include 'DIMENSIONS'
3014 use control_data,only:out1file
3018 ! include 'COMMON.LOCAL'
3019 ! include 'COMMON.VAR'
3020 ! include 'COMMON.CHAIN'
3021 ! include 'COMMON.INTERACT'
3022 ! include 'COMMON.IOUNITS'
3023 ! include 'COMMON.GEO'
3024 ! include 'COMMON.NAMES'
3025 ! include 'COMMON.CONTROL'
3026 ! include 'COMMON.SETUP'
3027 real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3030 integer :: i,j,it,iti
3031 real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3034 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3038 if (itype(i,1).ne.10) then
3040 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3044 dc_norm(j,i+nres)=0.0d0
3049 costtab(i+1) =dcos(theta(i+1))
3050 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3051 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3052 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3053 cosfac2=0.5d0/(1.0d0+costtab(i+1))
3054 cosfac=dsqrt(cosfac2)
3055 sinfac2=0.5d0/(1.0d0-costtab(i+1))
3056 sinfac=dsqrt(sinfac2)
3059 if ((it.ne.10).and.(it.ne.ntyp1)) then
3060 !el if (it.ne.10) then
3062 ! Compute the axes of tghe local cartesian coordinates system; store in
3063 ! x_prime, y_prime and z_prime
3071 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3072 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3074 call vecpr(x_prime,y_prime,z_prime)
3076 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3077 ! to local coordinate system. Store in xx, yy, zz.
3083 xx = xx + x_prime(j)*dc_norm(j,i+nres)
3084 yy = yy + y_prime(j)*dc_norm(j,i+nres)
3085 zz = zz + z_prime(j)*dc_norm(j,i+nres)
3100 if(me.eq.king.or..not.out1file) &
3101 write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3107 end subroutine sc_loc_geom
3108 !-----------------------------------------------------------------------------
3109 subroutine sccenter(ires,nscat,sccor)
3110 ! implicit real*8 (a-h,o-z)
3111 ! include 'DIMENSIONS'
3112 ! include 'COMMON.CHAIN'
3113 integer :: i,j,ires,nscat
3114 real(kind=8),dimension(3,20) :: sccor
3115 real(kind=8) :: sccmj
3116 ! print *,"I am in sccenter",ires,nscat
3120 sccmj=sccmj+sccor(j,i)
3121 !C print *,"insccent", ires,sccor(j,i)
3123 dc(j,ires)=sccmj/nscat
3126 end subroutine sccenter
3127 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3128 !-----------------------------------------------------------------------------
3129 subroutine bond_regular
3131 ! implicit real*8 (a-h,o-z)
3132 ! include 'DIMENSIONS'
3133 ! include 'COMMON.VAR'
3134 ! include 'COMMON.LOCAL'
3135 ! include 'COMMON.CALC'
3136 ! include 'COMMON.INTERACT'
3137 ! include 'COMMON.CHAIN'
3141 vbld_inv(i+1)=1.0d0/vbld(i+1)
3142 vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3143 vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3144 ! print *,vbld(i+1),vbld(i+1+nres)
3147 end subroutine bond_regular
3149 !-----------------------------------------------------------------------------
3151 !-----------------------------------------------------------------------------
3152 subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3153 ! This subroutine calculates unit vectors of a local reference system
3154 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3155 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3156 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3157 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3158 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3159 ! form a linear fragment. Returns vectors e1, e2, and e3.
3160 ! implicit real*8 (a-h,o-z)
3161 ! include 'DIMENSIONS'
3163 real(kind=8),dimension(3) :: e1,e2,e3
3164 real(kind=8),dimension(3) :: u,z
3165 ! include 'COMMON.IOUNITS'
3166 ! include 'COMMON.CHAIN'
3167 real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3169 integer :: i,i1,i2,i3,i4
3170 real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3183 if (s1.gt.coinc) goto 2
3184 write (iout,1000) i2,i3,i1
3189 2 if (s2.gt.coinc) goto 4
3190 write(iout,1000) i3,i4,i1
3197 v1=z(2)*u(3)-z(3)*u(2)
3198 v2=z(3)*u(1)-z(1)*u(3)
3199 v3=z(1)*u(2)-z(2)*u(1)
3200 anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3201 if (anorm.gt.align) goto 6
3202 write (iout,1010) i2,i3,i4,i1
3214 e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3215 e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3216 e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3217 1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3218 'coordinates of atom',i4,' are set to zero.')
3219 1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3220 ' fragment. coordinates of atom',i4,' are set to zero.')
3222 end subroutine refsys
3223 !-----------------------------------------------------------------------------
3225 !-----------------------------------------------------------------------------
3226 subroutine int_to_cart
3227 !--------------------------------------------------------------
3228 ! This subroutine converts the energy derivatives from internal
3229 ! coordinates to cartesian coordinates
3230 !-------------------------------------------------------------
3231 ! implicit real*8 (a-h,o-z)
3232 ! include 'DIMENSIONS'
3233 ! include 'COMMON.VAR'
3234 ! include 'COMMON.CHAIN'
3235 ! include 'COMMON.DERIV'
3236 ! include 'COMMON.GEO'
3237 ! include 'COMMON.LOCAL'
3238 ! include 'COMMON.INTERACT'
3239 ! include 'COMMON.MD'
3240 ! include 'COMMON.IOUNITS'
3241 ! include 'COMMON.SCCOR'
3242 ! calculating dE/ddc1
3245 ! print *,"gloc",gloc(:,:)
3246 ! print *, "gcart",gcart(:,:)
3247 if (nres.lt.3) go to 18
3249 gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3250 +gloc(nres-2,icg)*dtheta(j,1,3)
3251 if ((itype(2,1).ne.10).and.&
3252 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3253 gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3254 gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3257 ! Calculating the remainder of dE/ddc2
3259 gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3260 gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3261 if(itype(2,1).ne.10) then
3262 gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3263 gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3265 if(itype(3,1).ne.10) then
3266 gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3267 gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3270 gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3273 ! If there are only five residues
3276 gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3277 dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3279 ! if(itype(3,1).ne.10) then
3280 if ((itype(3,1).ne.10).and.&
3281 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3282 gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3283 dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3285 ! if(itype(4,1).ne.10) then
3286 if ((itype(4,1).ne.10).and.&
3287 (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3288 gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3289 dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3293 ! If there are more than five residues
3297 gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3298 +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3299 gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3300 gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3301 if(itype(i,1).ne.10) then
3302 gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3303 gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3305 if(itype(i+1,1).ne.10) then
3306 gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3307 +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3312 ! Setting dE/ddnres-2
3315 gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3316 dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3317 +gloc(2*nres-6,icg)* &
3318 dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3319 if(itype(nres-2,1).ne.10) then
3320 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3321 dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3324 if(itype(nres-1,1).ne.10) then
3325 gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3326 dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3331 ! Settind dE/ddnres-1
3333 gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3334 gloc(2*nres-5,icg)*dtheta(j,2,nres)
3335 if(itype(nres-1,1).ne.10) then
3336 gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3337 dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3341 ! The side-chain vector derivatives
3343 if(itype(i,1).ne.10 .and. &
3344 itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3346 gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3347 +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3351 !----------------------------------------------------------------------
3352 ! INTERTYP=1 SC...Ca...Ca...Ca
3353 ! INTERTYP=2 Ca...Ca...Ca...SC
3354 ! INTERTYP=3 SC...Ca...Ca...SC
3355 ! calculating dE/ddc1
3359 ! write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3361 if (nres.lt.2) return
3362 if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3363 if ((itype(1,1).ne.10).and. &
3364 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3366 !c Derviative was calculated for oposite vector of side chain therefore
3367 ! there is "-" sign before gloc_sc
3368 gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3370 gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3372 if ((itype(2,1).ne.10).and. &
3373 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3374 gxcart(j,1)= gxcart(j,1) &
3375 -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3376 gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3381 if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3382 (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3385 gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3388 ! As potetnial DO NOT depend on omicron anlge their derivative is
3390 ! & +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3392 ! Calculating the remainder of dE/ddc2
3394 if((itype(2,1).ne.10).and. &
3395 (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3396 if ((itype(1,1).ne.10).and.&
3397 ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3398 gxcart(j,2)=gxcart(j,2)+ &
3399 gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3400 if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3402 gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3403 !c the - above is due to different vector direction
3404 gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3407 ! if ((itype(1,1).ne.10).and.&
3408 ! ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3409 gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3410 !c the - above is due to different vector direction
3411 gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3412 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3413 ! write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3416 if ((itype(1,1).ne.10).and.&
3417 (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3418 gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3419 ! write(iout,*) gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3421 if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3422 gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3423 ! write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3425 if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3426 gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3427 ! write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3430 ! write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3432 ! If there are more than five residues
3436 ! write(iout,*) "before", gcart(j,i)
3437 if ((itype(i,1).ne.10).and.&
3438 (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3439 gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3440 *dtauangle(j,2,3,i+1) &
3441 -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3442 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3443 *dtauangle(j,1,2,i+2)
3444 ! write(iout,*) "new",j,i,
3445 ! & gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3446 ! if (itype(i-1,1).ne.10) then
3447 if ((itype(i-1,1).ne.10).and.&
3448 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3450 gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3451 *dtauangle(j,3,3,i+1)
3453 ! if (itype(i+1,1).ne.10) then
3454 if ((itype(i+1,1).ne.10).and.&
3455 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3456 gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3457 *dtauangle(j,3,1,i+2)
3458 gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3459 *dtauangle(j,3,2,i+2)
3462 ! if (itype(i-1,1).ne.10) then
3463 if ((itype(i-1,1).ne.10).and.&
3464 (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3465 gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3466 dtauangle(j,1,3,i+1)
3468 ! if (itype(i+1,1).ne.10) then
3469 if ((itype(i+1,1).ne.10).and.&
3470 (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3471 gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3472 dtauangle(j,2,2,i+2)
3473 ! write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3474 ! & dtauangle(j,2,2,i+2)
3476 ! if (itype(i+2,1).ne.10) then
3477 if ((itype(i+2,1).ne.10).and.&
3478 (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3479 gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3480 dtauangle(j,2,1,i+3)
3485 ! Setting dE/ddnres-1
3488 if ((itype(nres-1,1).ne.10).and.&
3489 (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3490 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3491 *dtauangle(j,2,3,nres)
3492 ! write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3493 ! & dtauangle(j,2,3,nres), gxcart(j,nres-1)
3494 ! if (itype(nres-2,1).ne.10) then
3495 if ((itype(nres-2,1).ne.10).and.&
3496 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3497 gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3498 *dtauangle(j,3,3,nres)
3500 if ((itype(nres,1).ne.10).and.&
3501 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3502 gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3503 *dtauangle(j,3,1,nres+1)
3504 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3505 *dtauangle(j,3,2,nres+1)
3508 if ((itype(nres-2,1).ne.10).and.&
3509 (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3510 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3511 dtauangle(j,1,3,nres)
3513 if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3514 gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3515 dtauangle(j,2,2,nres+1)
3516 ! write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3517 ! & dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3522 if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3523 (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3525 gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3526 *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3527 *dtauangle(j,2,3,nres+1)
3530 ! The side-chain vector derivatives
3531 ! print *,"gcart",gcart(:,:)
3533 end subroutine int_to_cart
3534 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3535 !-----------------------------------------------------------------------------
3537 !-----------------------------------------------------------------------------
3538 subroutine gen_dist_constr
3539 ! Generate CA distance constraints.
3540 ! implicit real*8 (a-h,o-z)
3541 ! include 'DIMENSIONS'
3542 ! include 'COMMON.IOUNITS'
3543 ! include 'COMMON.GEO'
3544 ! include 'COMMON.VAR'
3545 ! include 'COMMON.INTERACT'
3546 ! include 'COMMON.LOCAL'
3547 ! include 'COMMON.NAMES'
3548 ! include 'COMMON.CHAIN'
3549 ! include 'COMMON.FFIELD'
3550 ! include 'COMMON.SBRIDGE'
3551 ! include 'COMMON.HEADER'
3552 ! include 'COMMON.CONTROL'
3553 ! include 'COMMON.DBASE'
3554 ! include 'COMMON.THREAD'
3555 ! include 'COMMON.TIME1'
3556 ! integer :: itype_pdb !(maxres)
3557 ! common /pizda/ itype_pdb(nres)
3558 character(len=2) :: iden
3561 !d print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3562 !d write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3563 !d & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3565 do i=nstart_sup,nstart_sup+nsup-1
3566 !d write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3567 !d & ' seq_pdb', restyp(itype_pdb(i))
3568 do j=i+2,nstart_sup+nsup-1
3570 ihpb(nhpb)=i+nstart_seq-nstart_sup
3571 jhpb(nhpb)=j+nstart_seq-nstart_sup
3573 dhpb(nhpb)=dist(i,j)
3576 !d write (iout,'(a)') 'Distance constraints:'
3581 !d if (ii.gt.nres) then
3586 !d write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3587 !d & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3588 !d & dhpb(i),forcon(i)
3590 ! deallocate(itype_pdb)
3593 end subroutine gen_dist_constr
3595 !-----------------------------------------------------------------------------
3597 !-----------------------------------------------------------------------------
3598 subroutine cartprint
3600 use geometry_data, only: c
3601 use energy_data, only: itype
3602 ! implicit real*8 (a-h,o-z)
3603 ! include 'DIMENSIONS'
3604 ! include 'COMMON.CHAIN'
3605 ! include 'COMMON.INTERACT'
3606 ! include 'COMMON.NAMES'
3607 ! include 'COMMON.IOUNITS'
3612 write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3613 c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3615 100 format (//' alpha-carbon coordinates ',&
3616 ' centroid coordinates'/ &
3617 ' ', 6X,'X',11X,'Y',11X,'Z',&
3618 10X,'X',11X,'Y',11X,'Z')
3619 110 format (a,'(',i3,')',6f12.5)
3621 end subroutine cartprint
3622 !-----------------------------------------------------------------------------
3623 !-----------------------------------------------------------------------------
3624 subroutine alloc_geo_arrays
3625 !EL Allocation of tables used by module energy
3627 integer :: i,j,nres2
3631 allocate(phibound(2,nres+2)) !(2,maxres)
3632 !----------------------
3634 ! common /chain/ in molread
3635 ! real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3636 ! real(kind=8),dimension(:,:),allocatable :: dc
3637 allocate(dc_old(3,0:nres2))
3638 ! if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3639 if(.not.allocated(dc_norm2)) then
3640 allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3644 !el if(.not.allocated(dc_norm))
3645 !elwrite(iout,*) "jestem w alloc geo 1"
3646 if(.not.allocated(dc_norm)) then
3647 allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3650 !elwrite(iout,*) "jestem w alloc geo 1"
3651 allocate(xloc(3,nres),xrot(3,nres))
3652 !elwrite(iout,*) "jestem w alloc geo 1"
3654 !elwrite(iout,*) "jestem w alloc geo 1"
3655 allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3657 allocate(t(3,3,nres),r(3,3,nres))
3658 allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3659 ! common /refstruct/
3660 if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3661 !elwrite(iout,*) "jestem w alloc geo 2"
3662 allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3663 if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3664 if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3665 ! common /from_zscore/ in module.compare
3666 !----------------------
3668 ! Inverses of the actual virtual bond lengths
3669 ! common /invlen/ in io_conf: molread or readpdb
3670 ! real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3671 !----------------------
3673 ! Store the geometric variables in the following COMMON block.
3674 ! common /var/ in readpdb or ...
3675 if(.not.allocated(theta)) allocate(theta(nres+2))
3676 if(.not.allocated(phi)) allocate(phi(nres+2))
3677 if(.not.allocated(alph)) allocate(alph(nres+2))
3678 if(.not.allocated(omeg)) allocate(omeg(nres+2))
3679 if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3680 if(.not.allocated(phiref)) allocate(phiref(nres+2))
3681 if(.not.allocated(costtab)) allocate(costtab(nres))
3682 if(.not.allocated(sinttab)) allocate(sinttab(nres))
3683 if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3684 if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3685 ! real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3686 allocate(omicron(2,nres+2)) !(2,maxres)
3687 allocate(tauangle(3,nres+2)) !(3,maxres)
3688 !elwrite(iout,*) "jestem w alloc geo 3"
3689 if(.not.allocated(xxtab)) allocate(xxtab(nres))
3690 if(.not.allocated(yytab)) allocate(yytab(nres))
3691 if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3692 if(.not.allocated(xxref)) allocate(xxref(nres))
3693 if(.not.allocated(yyref)) allocate(yyref(nres))
3694 if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3695 allocate(ialph(nres,2)) !(maxres,2)
3698 allocate(ivar(4*nres2)) !(4*maxres2)
3700 #if defined(WHAM_RUN) || defined(CLUSTER)
3701 allocate(vbld(2*nres))
3703 allocate(vbld_inv(2*nres))
3708 end subroutine alloc_geo_arrays
3709 !-----------------------------------------------------------------------------
3710 !-----------------------------------------------------------------------------