source/unres/geometry.F90

   1                       module geometry
   2 !-----------------------------------------------------------------------------
   3       use io_units
   4       use names
   5       use math
   6       use MPI_data
   7       use geometry_data
   8       use control_data
   9       use energy_data
  10       implicit none
  11 !-----------------------------------------------------------------------------
  12 ! commom.bounds
  13 !      common /bounds/
  14 !-----------------------------------------------------------------------------
  15 ! commom.chain
  16 !      common /chain/
  17 !      common /rotmat/
  18       real(kind=8),dimension(:,:,:),allocatable :: t,r !(3,3,maxres)
  19 !-----------------------------------------------------------------------------
  20 ! common.geo
  21 !      common /geo/
  22 !-----------------------------------------------------------------------------
  23 ! common.locmove
  24 !     Variables (set in init routine) never modified by local_move
  25 !      common /loc_const/
  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
  32 !      common /loc_work/
  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 !-----------------------------------------------------------------------------
  43 !
  44 !
  45 !-----------------------------------------------------------------------------
  46       contains
  47 !-----------------------------------------------------------------------------
  48 ! arcos.f
  49 !-----------------------------------------------------------------------------
  50       real(kind=8) function ARCOS(X)
  51 !      implicit real*8 (a-h,o-z)
  52 !      include 'COMMON.GEO'
  53 !el local variables
  54       real(kind=8) :: x
  55       IF (DABS(X).LT.1.0D0) GOTO 1
  56       ARCOS=PIPOL*(1.0d0-DSIGN(1.0D0,X))
  57       RETURN
  58     1 ARCOS=DACOS(X)
  59       return
  60       end function ARCOS
  61 !-----------------------------------------------------------------------------
  62 ! chainbuild.F
  63 !-----------------------------------------------------------------------------
  64       subroutine chainbuild
  65 !
  66 ! Build the virtual polypeptide chain. Side-chain centroids are moveable.
  67 ! As of 2/17/95.
  68 !
  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'
  78       logical :: lprn
  79 !el local variables
  80       integer :: i,j
  81       real(kind=8) :: be,be1,alfai
  82       integer :: nres2
  83       nres2=2*nres
  84 ! Set lprn=.true. for debugging
  85       lprn = .false.
  86       print *,"I ENTER CHAINBUILD"
  87 !
  88 ! Define the origin and orientation of the coordinate system and locate the
  89 ! first three CA's and SC(2).
  90 !
  91 !elwrite(iout,*)"in chainbuild"
  92       call orig_frame
  93 !elwrite(iout,*)"after orig_frame"
  94 !
  95 ! Build the alpha-carbon chain.
  96 !
  97       do i=4,nres
  98         call locate_next_res(i)
  99       enddo
 100 !elwrite(iout,*)"after locate_next_res"
 101 !
 102 ! First and last SC must coincide with the corresponding CA.
 103 !
 104       do j=1,3
 105         dc(j,nres+1)=0.0D0
 106         dc_norm(j,nres+1)=0.0D0
 107         dc(j,nres+nres)=0.0D0
 108         dc_norm(j,nres+nres)=0.0D0
 109         c(j,nres+1)=c(j,1)
 110         c(j,nres+nres)=c(j,nres)
 111       enddo
 112 !
 113 ! Temporary diagnosis
 114 !
 115       if (lprn) then
 116
 117       call cartprint
 118       write (iout,'(/a)') 'Recalculated internal coordinates'
 119       do i=2,nres-1
 120         do j=1,3
 121           c(j,nres2+2)=0.5D0*(c(j,i-1)+c(j,i+1))        !maxres2=2*maxres
 122         enddo
 123         be=0.0D0
 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)
 126         alfai=0.0D0
 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
 130       enddo
 131  1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
 132
 133       endif
 134
 135       return
 136       end subroutine chainbuild
 137 !-----------------------------------------------------------------------------
 138       subroutine orig_frame
 139 !
 140 ! Define the origin and orientation of the coordinate system and locate
 141 ! the first three atoms.
 142 !
 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'
 149 !el local variables
 150       integer :: i,j
 151       real(kind=8) :: cost,sint
 152
 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)
 158
 159       cost=dcos(theta(3))
 160       sint=dsin(theta(3))
 161       t(1,1,1)=-cost
 162       t(1,2,1)=-sint
 163       t(1,3,1)= 0.0D0
 164       t(2,1,1)=-sint
 165       t(2,2,1)= cost
 166       t(2,3,1)= 0.0D0
 167       t(3,1,1)= 0.0D0
 168       t(3,2,1)= 0.0D0
 169       t(3,3,1)= 1.0D0
 170       r(1,1,1)= 1.0D0
 171       r(1,2,1)= 0.0D0
 172       r(1,3,1)= 0.0D0
 173       r(2,1,1)= 0.0D0
 174       r(2,2,1)= 1.0D0
 175       r(2,3,1)= 0.0D0
 176       r(3,1,1)= 0.0D0
 177       r(3,2,1)= 0.0D0
 178       r(3,3,1)= 1.0D0
 179       do i=1,3
 180         do j=1,3
 181           rt(i,j,1)=t(i,j,1)
 182         enddo
 183       enddo
 184       do i=1,3
 185         do j=1,3
 186           prod(i,j,1)=0.0D0
 187           prod(i,j,2)=t(i,j,1)
 188         enddo
 189         prod(i,i,1)=1.0D0
 190       enddo
 191       c(1,1)=0.0D0
 192       c(2,1)=0.0D0
 193       c(3,1)=0.0D0
 194       c(1,2)=vbld(2)
 195       c(2,2)=0.0D0
 196       c(3,2)=0.0D0
 197       dc(1,0)=0.0d0
 198       dc(2,0)=0.0D0
 199       dc(3,0)=0.0D0
 200       dc(1,1)=vbld(2)
 201       dc(2,1)=0.0D0
 202       dc(3,1)=0.0D0
 203       dc_norm(1,0)=0.0D0
 204       dc_norm(2,0)=0.0D0
 205       dc_norm(3,0)=0.0D0
 206       dc_norm(1,1)=1.0D0
 207       dc_norm(2,1)=0.0D0
 208       dc_norm(3,1)=0.0D0
 209       do j=1,3
 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)
 213       enddo
 214       call locate_side_chain(2)
 215       return
 216       end subroutine orig_frame
 217 !-----------------------------------------------------------------------------
 218       subroutine locate_next_res(i)
 219 !
 220 ! Locate CA(i) and SC(i-1)
 221 !
 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'
 231 !
 232 ! Define the rotation matrices corresponding to CA(i)
 233 !
 234 !el local variables
 235       integer :: i,j
 236       real(kind=8) :: theti,phii
 237       real(kind=8) :: cost,sint,cosphi,sinphi
 238 #ifdef OSF
 239 #ifdef WHAM_RUN
 240       theti=theta(i)
 241       icrc=0
 242       call proc_proc(theti,icrc)
 243       if(icrc.eq.1)theti=100.0
 244       phii=phi(i)
 245       icrc=0
 246       call proc_proc(phii,icrc)
 247       if(icrc.eq.1)phii=180.0
 248 #else
 249       theti=theta(i)
 250       if (theti.ne.theti) theti=100.0
 251       phii=phi(i)
 252       if (phii.ne.phii) phii=180.0
 253 #endif
 254 #else
 255       theti=theta(i)
 256       phii=phi(i)
 257 #endif
 258       cost=dcos(theti)
 259       sint=dsin(theti)
 260       cosphi=dcos(phii)
 261       sinphi=dsin(phii)
 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
 265       t(1,1,i-2)=-cost
 266       t(1,2,i-2)=-sint
 267       t(1,3,i-2)= 0.0D0
 268       t(2,1,i-2)=-sint
 269       t(2,2,i-2)= cost
 270       t(2,3,i-2)= 0.0D0
 271       t(3,1,i-2)= 0.0D0
 272       t(3,2,i-2)= 0.0D0
 273       t(3,3,i-2)= 1.0D0
 274       r(1,1,i-2)= 1.0D0
 275       r(1,2,i-2)= 0.0D0
 276       r(1,3,i-2)= 0.0D0
 277       r(2,1,i-2)= 0.0D0
 278       r(2,2,i-2)=-cosphi
 279       r(2,3,i-2)= sinphi
 280       r(3,1,i-2)= 0.0D0
 281       r(3,2,i-2)= sinphi
 282       r(3,3,i-2)= cosphi
 283       rt(1,1,i-2)=-cost
 284       rt(1,2,i-2)=-sint
 285       rt(1,3,i-2)=0.0D0
 286       rt(2,1,i-2)=sint*cosphi
 287       rt(2,2,i-2)=-cost*cosphi
 288       rt(2,3,i-2)=sinphi
 289       rt(3,1,i-2)=-sint*sinphi
 290       rt(3,2,i-2)=cost*sinphi
 291       rt(3,3,i-2)=cosphi
 292       call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
 293       do j=1,3
 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)
 297       enddo
 298 !d    print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
 299 !
 300 ! Now calculate the coordinates of SC(i-1)
 301 !
 302       call locate_side_chain(i-1)
 303       return
 304       end subroutine locate_next_res
 305 !-----------------------------------------------------------------------------
 306       subroutine locate_side_chain(i)
 307 !
 308 ! Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
 309 !
 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'
 319       integer :: i,j,k
 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))
 326       dsci=vbld(i+nres)
 327       dsci_inv=vbld_inv(i+nres)
 328 #ifdef OSF
 329       alphi=alph(i)
 330       omegi=omeg(i)
 331 #ifdef WHAM_RUN
 332 ! detecting NaNQ
 333       icrc=0
 334       call proc_proc(alphi,icrc)
 335       if(icrc.eq.1)alphi=100.0
 336       icrc=0
 337       call proc_proc(omegi,icrc)
 338       if(icrc.eq.1)omegi=-100.0
 339 #else
 340       if (alphi.ne.alphi) alphi=100.0
 341       if (omegi.ne.omegi) omegi=-100.0
 342 #endif
 343 #else
 344       alphi=alph(i)
 345       omegi=omeg(i)
 346 #endif
 347       cosalphi=dcos(alphi)
 348       sinalphi=dsin(alphi)
 349       cosomegi=dcos(omegi)
 350       sinomegi=dsin(omegi)
 351       xp= dsci*cosalphi
 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)
 357       cost2=dcos(theta2)
 358       sint2=dsin(theta2)
 359       xx(1)= xp*cost2+yp*sint2
 360       xx(2)=-xp*sint2+yp*cost2
 361       xx(3)= zp
 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)
 364       do j=1,3
 365         xloc(j,i)=xx(j)
 366       enddo
 367 ! Bring the SC vectors to the common coordinate system.
 368       xx(1)=xloc(1,i)
 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)
 371       do j=1,3
 372         xrot(j,i)=xx(j)
 373       enddo
 374       do j=1,3
 375         rj=0.0D0
 376         do k=1,3
 377           rj=rj+prod(j,k,i-1)*xx(k)
 378         enddo
 379         dc(j,nres+i)=rj
 380         dc_norm(j,nres+i)=rj*dsci_inv
 381         c(j,nres+i)=c(j,i)+rj
 382       enddo
 383       return
 384       end subroutine locate_side_chain
 385 !-----------------------------------------------------------------------------
 386 ! checkder_p.F
 387 !-----------------------------------------------------------------------------
 388       subroutine int_from_cart1(lprn)
 389 !      implicit real*8 (a-h,o-z)
 390 !      include 'DIMENSIONS'
 391 #ifdef MPI
 392       include 'mpif.h'
 393       integer :: ierror
 394 #endif
 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'
 404       logical :: lprn
 405 !el local variables
 406       integer :: i,j
 407       real(kind=8) :: dnorm1,dnorm2,be
 408       integer :: nres2
 409       nres2=2*nres
 410       if (lprn) write (iout,'(/a)') 'Recalculated internal coordinates'
 411 #ifdef TIMING
 412       time01=MPI_Wtime()
 413 #endif
 414
 415 #ifdef WHAM_RUN
 416       vbld(nres+1)=0.0d0
 417 !write(iout,*)"geometry warring, vbld=",(vbld(i),i=1,nres+1)
 418       vbld(2*nres)=0.0d0
 419       vbld_inv(nres+1)=0.0d0
 420       vbld_inv(2*nres)=0.0d0
 421 #endif
 422
 423 #if defined(PARINT) && defined(MPI)
 424       do i=iint_start,iint_end
 425 #else
 426       do i=2,nres
 427 #endif
 428         dnorm1=dist(i-1,i)
 429         dnorm2=dist(i,i+1)
 430         do j=1,3
 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)
 433         enddo
 434         be=0.0D0
 435         if (i.gt.2) then
 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)
 439         endif
 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)
 444         endif
 445         if (itype(i,1).ne.10) then
 446          tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
 447         endif
 448         endif
 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)
 452         vbld(i)=dist(i-1,i)
 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)
 458         else
 459           vbld_inv(nres+i)=0.0d0
 460         endif
 461       enddo
 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"
 468 !d       call flush(iout)
 469        time00=MPI_Wtime()
 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"
 474 !d       call flush(iout)
 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"
 479 !d       call flush(iout)
 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"
 484 !d       call flush(iout)
 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"
 489 !d       call flush(iout)
 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"
 494 !d       call flush(iout)
 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)
 498 #ifdef CRYST_SC
 499 !d       write (iout,*) "Gather alph"
 500 !d       call flush(iout)
 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"
 505 !d       call flush(iout)
 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)
 509 #endif
 510        time_gather=time_gather+MPI_Wtime()-time00
 511       endif
 512 #endif
 513       do i=1,nres-1
 514         do j=1,3
 515 !#ifdef WHAM_RUN
 516 #if defined(WHAM_RUN) || defined(CLUSTER)
 517           dc(j,i)=c(j,i+1)-c(j,i)
 518 #endif
 519           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 520         enddo
 521       enddo
 522       do i=2,nres-1
 523         do j=1,3
 524 !#ifdef WHAM_RUN
 525 #if defined(WHAM_RUN) || defined(CLUSTER)
 526           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 527 #endif
 528           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 529         enddo
 530       enddo
 531       if (lprn) then
 532       do i=2,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)
 536       enddo
 537       endif
 538  1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
 539 #ifdef TIMING
 540       time_intfcart=time_intfcart+MPI_Wtime()-time01
 541 #endif
 542       return
 543       end subroutine int_from_cart1
 544 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 545 !-----------------------------------------------------------------------------
 546 ! check_sc_distr.f
 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'
 557       logical :: fail
 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
 563 !el local variables
 564       integer :: it,i,j,isample,indal,indom
 565       real(kind=8) :: al,om,dV
 566       dV=2.0D0*5.0D0*deg2rad*deg2rad
 567       print *,'dv=',dv
 568       do 10 it=1,1
 569         if ((it.eq.10).or.(it.eq.ntyp1)) goto 10
 570         open (20,file=restyp(it,1)//'_distr.sdc',status='unknown')
 571         call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
 572         close (20)
 573         goto 10
 574         open (20,file=restyp(it,1)//'_distr1.sdc',status='unknown')
 575         do i=0,90
 576           do j=0,72
 577             prob(j,i)=0.0D0
 578           enddo
 579         enddo
 580         do isample=1,MaxSample
 581           call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
 582           indal=rad2deg*al/2
 583           indom=(rad2deg*om+180.0D0)/5
 584           prob(indom,indal)=prob(indom,indal)+delt
 585         enddo
 586         do i=45,90
 587           do j=0,72
 588             write (20,'(2f10.3,1pd15.5)') 2*i+0.0D0,5*j-180.0D0,&
 589                     prob(j,i)/dV
 590           enddo
 591         enddo
 592    10   continue
 593       return
 594       end subroutine check_sc_distr
 595 #endif
 596 !-----------------------------------------------------------------------------
 597 ! convert.f
 598 !-----------------------------------------------------------------------------
 599       subroutine geom_to_var(n,x)
 600 !
 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
 606 !    2*nres-4+nside
 607 ! 4. The torsional angles omega of SC orientation: 2*nres-4+nside+1
 608 !    thru 2*nre-4+2*nside
 609 !
 610 !      implicit real*8 (a-h,o-z)
 611 !      include 'DIMENSIONS'
 612 !      include 'COMMON.VAR'
 613 !      include 'COMMON.GEO'
 614 !      include 'COMMON.CHAIN'
 615       integer :: n,i
 616       real(kind=8),dimension(n) :: x
 617 !d    print *,'nres',nres,' nphi',nphi,' ntheta',ntheta,' nvar',nvar
 618       do i=4,nres
 619         x(i-3)=phi(i)
 620 !d      print *,i,i-3,phi(i)
 621       enddo
 622       if (n.eq.nphi) return
 623       do i=3,nres
 624         x(i-2+nphi)=theta(i)
 625 !d      print *,i,i-2+nphi,theta(i)
 626       enddo
 627       if (n.eq.nphi+ntheta) return
 628       do i=2,nres-1
 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)
 633         endif
 634       enddo
 635       return
 636       end subroutine geom_to_var
 637 !-----------------------------------------------------------------------------
 638       subroutine var_to_geom(n,x)
 639 !
 640 ! Update geometry parameters according to the variable array.
 641 !
 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'
 648       integer :: n,i,ii
 649       real(kind=8),dimension(n) :: x
 650       logical :: change !,reduce
 651 !el      alph=0.0d0
 652 !el      omeg=0.0d0
 653 !el      phi=0.0d0
 654 !el      theta=0.0d0
 655
 656       change=reduce(x)
 657       if (n.gt.nphi+ntheta) then
 658         do i=1,nside
 659           ii=ialph(i,2)
 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
 664         enddo
 665       endif
 666       do i=4,nres
 667         phi(i)=x(i-3)
 668 !elwrite(iout,*) "phi",i,phi
 669       enddo
 670       if (n.eq.nphi) return
 671       do i=3,nres
 672         theta(i)=x(i-2+nphi)
 673 !elwrite(iout,*) "theta",i,theta
 674         if (theta(i).eq.pi) theta(i)=0.99d0*pi
 675         x(i-2+nphi)=theta(i)
 676       enddo
 677       return
 678       end subroutine var_to_geom
 679 !-----------------------------------------------------------------------------
 680       logical function convert_side(alphi,omegi)
 681 !      implicit none
 682       real(kind=8) :: alphi,omegi
 683 !el      real(kind=8) :: pinorm
 684 !      include 'COMMON.GEO'
 685       convert_side=.false.
 686 ! Apply periodicity restrictions.
 687       if (alphi.gt.pi) then
 688         alphi=dwapi-alphi
 689         omegi=pinorm(omegi+pi)
 690         convert_side=.true.
 691       endif
 692       return
 693       end function convert_side
 694 !-----------------------------------------------------------------------------
 695       logical function reduce(x)
 696 !
 697 ! Apply periodic restrictions to variables.
 698 !
 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
 706       integer :: i,ii,iii
 707       zmiana=.false.
 708       do i=4,nres
 709         x(i-3)=pinorm(x(i-3))
 710       enddo
 711       if (nvar.gt.nphi+ntheta) then
 712         do i=1,nside
 713           ii=nphi+ntheta+i
 714           iii=ii+nside
 715           x(ii)=thetnorm(x(ii))
 716           x(iii)=pinorm(x(iii))
 717 ! Apply periodic restrictions.
 718           zm=convert_side(x(ii),x(iii))
 719           zmiana=zmiana.or.zm
 720         enddo
 721       endif
 722       if (nvar.eq.nphi) return
 723       do i=3,nres
 724         ii=i-2+nphi
 725         iii=i-3
 726         x(ii)=dmod(x(ii),dwapi)
 727 ! Apply periodic restrictions.
 728         if (x(ii).gt.pi) then
 729           zmiana=.true.
 730           x(ii)=dwapi-x(ii)
 731           if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
 732           if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
 733           ii=ialph(i-1,1)
 734           if (ii.gt.0) then
 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))
 738           endif
 739         else if (x(ii).lt.-pi) then
 740           zmiana=.true.
 741           x(ii)=dwapi+x(ii)
 742           ii=ialph(i-1,1)
 743           if (ii.gt.0) 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))
 747           endif
 748         else if (x(ii).lt.0.0d0) then
 749           zmiana=.true.
 750           x(ii)=-x(ii)
 751           if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
 752           if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
 753           ii=ialph(i-1,1)
 754           if (ii.gt.0) then
 755             x(ii+nside)=pinorm(-x(ii+nside))
 756             zm=convert_side(x(ii),x(ii+nside))
 757           endif
 758         endif
 759       enddo
 760       reduce=zmiana
 761       return
 762       end function reduce
 763 !-----------------------------------------------------------------------------
 764       real(kind=8) function thetnorm(x)
 765 ! This function puts x within [0,2Pi].
 766       implicit none
 767       real(kind=8) :: x,xx
 768 !      include 'COMMON.GEO'
 769       xx=dmod(x,dwapi)
 770       if (xx.lt.0.0d0) xx=xx+dwapi
 771       if (xx.gt.0.9999d0*pi) xx=0.9999d0*pi
 772       thetnorm=xx
 773       return
 774       end function thetnorm
 775 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 776 !-----------------------------------------------------------------------------
 777       subroutine var_to_geom_restr(n,xx)
 778 !
 779 ! Update geometry parameters according to the variable array.
 780 !
 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'
 787       integer :: n,i,ii
 788       real(kind=8),dimension(6*nres) :: x,xx !(maxvar) (maxvar=6*maxres)
 789       logical :: change !,reduce
 790
 791       call xx2x(x,xx)
 792       change=reduce(x)
 793       do i=1,nside
 794           ii=ialph(i,2)
 795           alph(ii)=x(nphi+ntheta+i)
 796           omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
 797       enddo
 798       do i=4,nres
 799         phi(i)=x(i-3)
 800       enddo
 801       do i=3,nres
 802         theta(i)=x(i-2+nphi)
 803         if (theta(i).eq.pi) theta(i)=0.99d0*pi
 804         x(i-2+nphi)=theta(i)
 805       enddo
 806       return
 807       end subroutine var_to_geom_restr
 808 !-----------------------------------------------------------------------------
 809 ! gen_rand_conf.F
 810 !-----------------------------------------------------------------------------
 811       subroutine gen_rand_conf(nstart,*)
 812 ! Generate random conformation or chain cut and regrowth.
 813       use mcm_data
 814       use random, only: iran_num,ran_number
 815 !      implicit real*8 (a-h,o-z)
 816 !      include 'DIMENSIONS'
 817 !      include 'COMMON.CHAIN'
 818 !      include 'COMMON.LOCAL'
 819 !      include 'COMMON.VAR'
 820 !      include 'COMMON.INTERACT'
 821 !      include 'COMMON.IOUNITS'
 822 !      include 'COMMON.MCM'
 823 !      include 'COMMON.GEO'
 824 !      include 'COMMON.CONTROL'
 825       logical :: back,fail      !overlap,
 826 !el local variables
 827       integer :: i,nstart,maxsi,nsi,maxnit,nit,niter
 828       integer :: it1,it2,it,j
 829 !d    print *,' CG Processor',me,' maxgen=',maxgen
 830       maxsi=1000
 831       write (iout,*) 'Gen_Rand_conf: nstart=',nstart,nres
 832       if (nstart.lt.5) then
 833         it1=iabs(itype(2,1))
 834         phi(4)=gen_phi(4,iabs(itype(2,1)),iabs(itype(3,1)))
 835 !       write(iout,*)'phi(4)=',rad2deg*phi(4)
 836         if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2,1)),pi,phi(4),molnum(2))
 837 !       write(iout,*)'theta(3)=',rad2deg*theta(3)
 838         if ((it1.ne.10).and.(it1.ne.ntyp1)) then
 839           nsi=0
 840           fail=.true.
 841           do while (fail.and.nsi.le.maxsi)
 842             call gen_side(it1,theta(3),alph(2),omeg(2),fail,molnum(2))
 843             write (iout,*) 'nsi=',nsi,maxsi
 844             nsi=nsi+1
 845           enddo
 846           if (nsi.gt.maxsi) return 1
 847         endif ! it1.ne.10
 848         write(iout,*) "before origin_frame"
 849         call orig_frame
 850         write(iout,*) "after origin_frame"
 851         i=4
 852         nstart=4
 853       else
 854         i=nstart
 855         nstart=max0(i,4)
 856       endif
 857
 858       maxnit=0
 859
 860       nit=0
 861       niter=0
 862       back=.false.
 863       do while (i.le.nres .and. niter.lt.maxgen)
 864         write(iout,*) 'i=',i,'back=',back
 865         if (i.lt.nstart) then
 866           if(iprint.gt.1) then
 867           write (iout,'(/80(1h*)/2a/80(1h*))') &
 868                 'Generation procedure went down to ',&
 869                 'chain beginning. Cannot continue...'
 870           write (*,'(/80(1h*)/2a/80(1h*))') &
 871                 'Generation procedure went down to ',&
 872                 'chain beginning. Cannot continue...'
 873           endif
 874           return 1
 875         endif
 876         it1=iabs(itype(i-1,molnum(i-1)))
 877         it2=iabs(itype(i-2,molnum(i-2)))
 878         it=iabs(itype(i,molnum(i)))
 879         if ((it.eq.ntyp1).and.(it1.eq.ntyp1)) &
 880           vbld(i)=ran_number(30.0D0,40.0D0)
 881 !       print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,&
 882 !        ' nit=',nit,' niter=',niter,' maxgen=',maxgen
 883         phi(i+1)=gen_phi(i+1,it1,it)
 884         if (back) then
 885           phi(i)=gen_phi(i+1,it2,it1)
 886 !         print *,'phi(',i,')=',phi(i)
 887           theta(i-1)=gen_theta(it2,phi(i-1),phi(i),molnum(i))
 888 !          print *,"theta",theta(i-1),phi(i)
 889           if ((it2.ne.10).and.(it2.ne.ntyp1)) then
 890             nsi=0
 891             fail=.true.
 892             do while (fail.and.nsi.le.maxsi)
 893               call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail,molnum(i-2))
 894               nsi=nsi+1
 895             enddo
 896             if (nsi.gt.maxsi) return 1
 897           endif
 898           call locate_next_res(i-1)
 899         endif
 900         theta(i)=gen_theta(it1,phi(i),phi(i+1),molnum(i))
 901 !        write(iout,*) "theta(i),",theta(i)
 902         if ((it1.ne.10).and.(it1.ne.ntyp1)) then
 903         nsi=0
 904         fail=.true.
 905         do while (fail.and.nsi.le.maxsi)
 906           call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail,molnum(i))
 907 !                  write(iout,*)"alpha,omeg(i-1)",alph(i-1),omeg(i-1),i,nsi,maxsi
 908           nsi=nsi+1
 909         enddo
 910         if (nsi.gt.maxsi) return 1
 911         endif
 912         call locate_next_res(i)
 913         write(iout,*) "overlap,",overlap(i-1)
 914         if (overlap(i-1)) then
 915           if (nit.lt.maxnit) then
 916             back=.true.
 917             nit=nit+1
 918           else
 919             nit=0
 920             if (i.gt.3) then
 921               back=.true.
 922               i=i-1
 923             else
 924               write (iout,'(a)') &
 925         'Cannot generate non-overlaping conformation. Increase MAXNIT.'
 926               write (*,'(a)') &
 927         'Cannot generate non-overlaping conformation. Increase MAXNIT.'
 928               return 1
 929             endif
 930           endif
 931         else
 932 !          write(iout,*) "tu dochodze"
 933           back=.false.
 934           nit=0
 935           i=i+1
 936         endif
 937         niter=niter+1
 938       enddo
 939       if (niter.ge.maxgen) then
 940         write (iout,'(a,2i5)') &
 941        'Too many trials in conformation generation',niter,maxgen
 942         write (*,'(a,2i5)') &
 943        'Too many trials in conformation generation',niter,maxgen
 944         return 1
 945       endif
 946       do j=1,3
 947         c(j,nres+1)=c(j,1)
 948         c(j,nres+nres)=c(j,nres)
 949       enddo
 950       return
 951       end subroutine gen_rand_conf
 952 !-----------------------------------------------------------------------------
 953       logical function overlap(i)
 954 !      implicit real*8 (a-h,o-z)
 955 !      include 'DIMENSIONS'
 956 !      include 'COMMON.CHAIN'
 957 !      include 'COMMON.INTERACT'
 958 !      include 'COMMON.FFIELD'
 959       integer :: i,j,iti,itj,iteli,itelj,k
 960       real(kind=8) :: redfac,rcomp
 961       integer :: nres2
 962       nres2=2*nres
 963       data redfac /0.5D0/
 964       overlap=.false.
 965       iti=iabs(itype(i,molnum(i)))
 966       if (iti.gt.ntyp) return
 967 ! Check for SC-SC overlaps.
 968 !d    print *,'nnt=',nnt,' nct=',nct
 969       do j=nnt,i-1
 970 !        print *, "molnum(j)",j,molnum(j)
 971         if (molnum(j).eq.1) then
 972         itj=iabs(itype(j,1))
 973         if (itj.eq.ntyp1) cycle
 974         if (j.lt.i-1 .or. ipot.ne.4) then
 975           rcomp=sigmaii(iti,itj)
 976         else
 977           rcomp=sigma(iti,itj)
 978         endif
 979 !d      print *,'j=',j
 980         if (dist(nres+i,nres+j).lt.redfac*rcomp) then
 981           overlap=.true.
 982
 983 !        print *,'overlap, SC-SC: i=',i,' j=',j,
 984 !     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
 985 !     &     rcomp
 986           return
 987         endif
 988         else if (molnum(j).eq.2) then
 989         itj=iabs(itype(j,2))
 990         if (dist(nres+i,nres+j).lt.redfac*sigma_nucl(iti,itj)) then
 991           overlap=.true.
 992
 993 !        print *,'overlap, SC-SC: i=',i,' j=',j,
 994 !     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
 995 !     &     rcomp
 996           return
 997         endif
 998
 999       endif
1000       enddo
1001 ! Check for overlaps between the added peptide group and the preceding
1002 ! SCs.
1003       iteli=itel(i)
1004       do j=1,3
1005 !       c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
1006         c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1007       enddo
1008       do j=nnt,i-2
1009         if (molnum(j).ne.1) cycle
1010         itj=iabs(itype(j,1))
1011 !d      print *,'overlap, p-Sc: i=',i,' j=',j,
1012 !d   &         ' dist=',dist(nres+j,maxres2+1)
1013         if (dist(nres+j,nres2+3).lt.4.0D0*redfac) then
1014           overlap=.true.
1015           return
1016         endif
1017       enddo
1018 ! Check for overlaps between the added side chain and the preceding peptide
1019 ! groups.
1020       do j=1,nnt-2
1021         if (molnum(j).ne.1) cycle
1022         do k=1,3
1023           c(k,nres2+3)=0.5D0*(c(k,j)+c(k,j+1))
1024         enddo
1025 !d      print *,'overlap, SC-p: i=',i,' j=',j,
1026 !d   &         ' dist=',dist(nres+i,maxres2+1)
1027         if (dist(nres+i,nres2+3).lt.4.0D0*redfac) then
1028           overlap=.true.
1029           return
1030         endif
1031       enddo
1032 ! Check for p-p overlaps
1033       do j=1,3
1034         c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1035       enddo
1036       do j=nnt,i-2
1037 !        if (molnum(j).eq.1) then
1038         itelj=itel(j)
1039         do k=1,3
1040           c(k,nres2+4)=0.5D0*(c(k,j)+c(k,j+1))
1041         enddo
1042 !d      print *,'overlap, p-p: i=',i,' j=',j,
1043 !d   &         ' dist=',dist(maxres2+1,maxres2+2)
1044         if (molnum(j).eq.1) then
1045         if(iteli.ne.0.and.itelj.ne.0)then
1046         if (dist(nres2+3,nres2+4).lt.rpp(iteli,itelj)*redfac) then
1047           overlap=.true.
1048           return
1049         endif
1050         endif
1051         else if (molnum(j).eq.2) then
1052         if (dist(nres2+3,nres2+4).lt.3.0) then
1053           overlap=.true.
1054           return
1055         endif
1056       endif
1057       enddo
1058       return
1059       end function overlap
1060 !-----------------------------------------------------------------------------
1061       real(kind=8) function gen_phi(i,it1,it2)
1062       use random, only:ran_number
1063 !      implicit real*8 (a-h,o-z)
1064 !      include 'DIMENSIONS'
1065 !      include 'COMMON.GEO'
1066 !      include 'COMMON.BOUNDS'
1067       integer :: i,it1,it2
1068 !      gen_phi=ran_number(-pi,pi)
1069 ! 8/13/98 Generate phi using pre-defined boundaries
1070       gen_phi=ran_number(phibound(1,i),phibound(2,i))
1071       return
1072       end function gen_phi
1073 !-----------------------------------------------------------------------------
1074       real(kind=8) function gen_theta(it,gama,gama1,mnum)
1075       use random,only:binorm,ran_number
1076 !      implicit real*8 (a-h,o-z)
1077 !      include 'DIMENSIONS'
1078 !      include 'COMMON.LOCAL'
1079 !      include 'COMMON.GEO'
1080       real(kind=8),dimension(2) :: y,z
1081       real(kind=8) :: theta_max,theta_min,sig,ak
1082 !el local variables
1083       integer :: j,it,k,mnum
1084       real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1085 !     print *,'gen_theta: it=',it
1086       theta_min=0.05D0*pi
1087       theta_max=0.95D0*pi
1088       if (dabs(gama).gt.dwapi) then
1089         y(1)=dcos(gama)
1090         y(2)=dsin(gama)
1091       else
1092         y(1)=0.0D0
1093         y(2)=0.0D0
1094       endif
1095       if (dabs(gama1).gt.dwapi) then
1096         z(1)=dcos(gama1)
1097         z(2)=dsin(gama1)
1098       else
1099         z(1)=0.0D0
1100         z(2)=0.0D0
1101       endif
1102       if (it.eq.ntyp1) then
1103       gen_theta=ran_number(theta_max/2.0,theta_max)
1104       else if (mnum.eq.1) then
1105
1106       thet_pred_mean=a0thet(it)
1107 !      write(iout,*),it,thet_pred_mean,"gen_thet"
1108       do k=1,2
1109         thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1110            +bthet(k,it,1,1)*z(k)
1111       enddo
1112       sig=polthet(3,it)
1113       do j=2,0,-1
1114         sig=sig*thet_pred_mean+polthet(j,it)
1115       enddo
1116       sig=0.5D0/(sig*sig+sigc0(it))
1117       ak=dexp(gthet(1,it)- &
1118        0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1119 !     print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1120 !     print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1121       theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1122       if (theta_temp.lt.theta_min) theta_temp=theta_min
1123       if (theta_temp.gt.theta_max) theta_temp=theta_max
1124       gen_theta=theta_temp
1125 !     print '(a)','Exiting GENTHETA.'
1126       else if (mnum.eq.2) then
1127        gen_theta=2.0d0 + ran_number(0.0d0,0.34d0)
1128       else
1129               gen_theta=ran_number(theta_max/2.0,theta_max)
1130        endif
1131       return
1132       end function gen_theta
1133 !-----------------------------------------------------------------------------
1134       subroutine gen_side(it,the,al,om,fail,mnum)
1135       use random, only:ran_number,mult_norm1
1136 !      implicit real*8 (a-h,o-z)
1137 !      include 'DIMENSIONS'
1138 !      include 'COMMON.GEO'
1139 !      include 'COMMON.LOCAL'
1140 !      include 'COMMON.SETUP'
1141 !      include 'COMMON.IOUNITS'
1142       real(kind=8) :: MaxBoxLen=10.0D0
1143       real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1144       real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1145       real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1146       real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1147       real(kind=8),dimension(2) :: y,cm,eig
1148       real(kind=8),dimension(2,2) :: box
1149       real(kind=8),dimension(100) :: work
1150       real(kind=8) :: eig_limit=1.0D-8
1151       real(kind=8) :: Big=10.0D0
1152       logical :: lprint,fail,lcheck
1153 !el local variables
1154       integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob,mnum
1155       real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1156       real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1157       real(kind=8) :: which_lobe
1158       lcheck=.false.
1159       lprint=.false.
1160       fail=.false.
1161       if (mnum.eq.1) then
1162       if (the.eq.0.0D0 .or. the.eq.pi) then
1163 #ifdef MPI
1164         write (*,'(a,i4,a,i3,a,1pe14.5)') &
1165        'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1166 #else
1167 !d        write (iout,'(a,i3,a,1pe14.5)')
1168 !d     &   'Error in GenSide: it=',it,' theta=',the
1169 #endif
1170         fail=.true.
1171         return
1172       endif
1173       if (nlobit.eq.0) then
1174          al=ran_number(0.05d0,pi/6)
1175          om=ran_number(-pi,pi)
1176          return
1177       endif
1178       tant=dtan(the-pipol)
1179       nlobit=nlob(it)
1180       allocate(z(3,nlobit))
1181       allocate(W1(nlobit))
1182       allocate(detAp(nlobit))
1183       allocate(sumW(0:nlobit))
1184       if (lprint) then
1185 #ifdef MPI
1186         print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1187         write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1188 #endif
1189         print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1190         write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1191            ' tant=',tant
1192       endif
1193       do i=1,nlobit
1194        zz1=tant-censc(1,i,it)
1195         do k=1,3
1196           do l=1,3
1197             a(k,l)=gaussc(k,l,i,it)
1198           enddo
1199         enddo
1200         detApi=a(2,2)*a(3,3)-a(2,3)**2
1201         Ap_inv(2,2)=a(3,3)/detApi
1202         Ap_inv(2,3)=-a(2,3)/detApi
1203         Ap_inv(3,2)=Ap_inv(2,3)
1204         Ap_inv(3,3)=a(2,2)/detApi
1205         if (lprint) then
1206           write (*,'(/a,i2/)') 'Cluster #',i
1207           write (*,'(3(1pe14.5),5x,1pe14.5)') &
1208           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1209           write (iout,'(/a,i2/)') 'Cluster #',i
1210           write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1211           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1212         endif
1213         W1i=0.0D0
1214         do k=2,3
1215           do l=2,3
1216             W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1217           enddo
1218         enddo
1219         W1i=a(1,1)-W1i
1220         W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1221 !        if (lprint) write(*,'(a,3(1pe15.5)/)')
1222 !     &          'detAp, W1, anormi',detApi,W1i,anormi
1223         do k=2,3
1224           zk=censc(k,i,it)
1225           do l=2,3
1226             zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1227           enddo
1228           z(k,i)=zk
1229         enddo
1230         detAp(i)=dsqrt(detApi)
1231       enddo
1232
1233       if (lprint) then
1234         print *,'W1:',(w1(i),i=1,nlobit)
1235         print *,'detAp:',(detAp(i),i=1,nlobit)
1236         print *,'Z'
1237         do i=1,nlobit
1238           print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1239         enddo
1240         write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1241         write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1242         write (iout,*) 'Z'
1243         do i=1,nlobit
1244           write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1245         enddo
1246       endif
1247       if (lcheck) then
1248 ! Writing the distribution just to check the procedure
1249       fac=0.0D0
1250       dV=deg2rad**2*10.0D0
1251       sum=0.0D0
1252       sum1=0.0D0
1253       do i=1,nlobit
1254         fac=fac+W1(i)/detAp(i)
1255       enddo
1256       fac=1.0D0/(2.0D0*fac*pi)
1257 !d    print *,it,'fac=',fac
1258       do ial=90,180,2
1259         y(1)=deg2rad*ial
1260         do iom=-180,180,5
1261           y(2)=deg2rad*iom
1262           wart=0.0D0
1263           do i=1,nlobit
1264             do j=2,3
1265               do k=2,3
1266                 a(j-1,k-1)=gaussc(j,k,i,it)
1267               enddo
1268             enddo
1269             y2=y(2)
1270
1271             do iii=-1,1
1272
1273               y(2)=y2+iii*dwapi
1274
1275               wykl=0.0D0
1276               do j=1,2
1277                 do k=1,2
1278                   wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1279                 enddo
1280               enddo
1281               wart=wart+W1(i)*dexp(-0.5D0*wykl)
1282
1283             enddo
1284
1285             y(2)=y2
1286
1287           enddo
1288 !         print *,'y',y(1),y(2),' fac=',fac
1289           wart=fac*wart
1290           write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1291           sum=sum+wart
1292           sum1=sum1+1.0D0
1293         enddo
1294       enddo
1295 !     print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1296       return
1297       endif
1298
1299 ! Calculate the CM of the system
1300 !
1301       do i=1,nlobit
1302         W1(i)=W1(i)/detAp(i)
1303       enddo
1304       sumW(0)=0.0D0
1305       do i=1,nlobit
1306         sumW(i)=sumW(i-1)+W1(i)
1307       enddo
1308       cm(1)=z(2,1)*W1(1)
1309       cm(2)=z(3,1)*W1(1)
1310       do j=2,nlobit
1311         cm(1)=cm(1)+z(2,j)*W1(j)
1312         cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1313       enddo
1314       cm(1)=cm(1)/sumW(nlobit)
1315       cm(2)=cm(2)/sumW(nlobit)
1316       if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1317        cm(2).gt.Big .or. cm(2).lt.-Big) then
1318 !d        write (iout,'(a)')
1319 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1320 !d        write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1321 !d        write (*,'(a)')
1322 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1323 !d        write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1324         fail=.true.
1325         return
1326       endif
1327 !d    print *,'CM:',cm(1),cm(2)
1328 !
1329 ! Find the largest search distance from CM
1330 !
1331       radmax=0.0D0
1332       do i=1,nlobit
1333         do j=2,3
1334           do k=2,3
1335             a(j-1,k-1)=gaussc(j,k,i,it)
1336           enddo
1337         enddo
1338 #ifdef NAG
1339         call f02faf('N','U',2,a,3,eig,work,100,ifail)
1340 #else
1341         call djacob(2,3,10000,1.0d-10,a,vec,eig)
1342 #endif
1343 #ifdef MPI
1344         if (lprint) then
1345           print *,'*************** CG Processor',me
1346           print *,'CM:',cm(1),cm(2)
1347           write (iout,*) '*************** CG Processor',me
1348           write (iout,*) 'CM:',cm(1),cm(2)
1349           print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1350           write (iout,'(A,8f10.5)') &
1351               'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1352         endif
1353 #endif
1354         if (eig(1).lt.eig_limit) then
1355           write(iout,'(a)') &
1356            'From Mult_Norm: Eigenvalues of A are too small.'
1357           write(*,'(a)') &
1358            'From Mult_Norm: Eigenvalues of A are too small.'
1359           fail=.true.
1360           return
1361         endif
1362         radius=0.0D0
1363 !d      print *,'i=',i
1364         do j=1,2
1365           radius=radius+pinorm(z(j+1,i)-cm(j))**2
1366         enddo
1367         radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1368         if (radius.gt.radmax) radmax=radius
1369       enddo
1370       if (radmax.gt.pi) radmax=pi
1371 !
1372 ! Determine the boundaries of the search rectangle.
1373 !
1374       if (lprint) then
1375         print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1376         print '(a,4(1pe14.4))','radmax: ',radmax
1377       endif
1378       box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1379       box(2,1)=dmin1(cm(1)+radmax,pi)
1380       box(1,2)=cm(2)-radmax
1381       box(2,2)=cm(2)+radmax
1382       if (lprint) then
1383 #ifdef MPI
1384         print *,'CG Processor',me,' Array BOX:'
1385 #else
1386         print *,'Array BOX:'
1387 #endif
1388         print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1389         print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1390 #ifdef MPI
1391         write (iout,*)'CG Processor',me,' Array BOX:'
1392 #else
1393         write (iout,*)'Array BOX:'
1394 #endif
1395         write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1396         write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1397       endif
1398 !      if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1399 !#ifdef MPI
1400 !        write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1401 !        write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1402 !#else
1403 !        write (iout,'(a)') 'Bad sampling box.'
1404 !#endif
1405 !        fail=.true.
1406 !        return
1407 !      endif
1408       which_lobe=ran_number(0.0D0,sumW(nlobit))
1409 !     print '(a,1pe14.4)','which_lobe=',which_lobe
1410       do i=1,nlobit
1411         if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1412       enddo
1413     1 ilob=i
1414 !     print *,'ilob=',ilob,' nlob=',nlob(it)
1415       do i=2,3
1416         cm(i-1)=z(i,ilob)
1417         do j=2,3
1418           a(i-1,j-1)=gaussc(i,j,ilob,it)
1419         enddo
1420       enddo
1421 !d    print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1422       call mult_norm1(3,2,a,cm,box,y,fail)
1423       if (fail) return
1424       al=y(1)
1425       om=pinorm(y(2))
1426       else if (mnum.eq.2) then
1427        al=0.7+ran_number(0.0d0,0.2d0)
1428        om=ran_number(0.0d0,3.14d0)
1429       endif
1430
1431 !d    print *,'al=',al,' om=',om
1432 !d    stop
1433       return
1434       end subroutine gen_side
1435 !-----------------------------------------------------------------------------
1436       subroutine overlap_sc(scfail)
1437 !
1438 !     Internal and cartesian coordinates must be consistent as input,
1439 !     and will be up-to-date on return.
1440 !     At the end of this procedure, scfail is true if there are
1441 !     overlapping residues left, or false otherwise (success)
1442 !
1443 !      implicit real*8 (a-h,o-z)
1444 !      include 'DIMENSIONS'
1445 !      include 'COMMON.CHAIN'
1446 !      include 'COMMON.INTERACT'
1447 !      include 'COMMON.FFIELD'
1448 !      include 'COMMON.VAR'
1449 !      include 'COMMON.SBRIDGE'
1450 !      include 'COMMON.IOUNITS'
1451       logical :: had_overlaps,fail,scfail
1452       integer,dimension(nres) :: ioverlap !(maxres)
1453       integer :: ioverlap_last,k,maxsi,i,iti,nsi
1454       integer :: ires,j
1455
1456       had_overlaps=.false.
1457       call overlap_sc_list(ioverlap,ioverlap_last)
1458       if (ioverlap_last.gt.0) then
1459         write (iout,*) '#OVERLAPing residues ',ioverlap_last
1460         write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1461         had_overlaps=.true.
1462       endif
1463
1464       maxsi=1000
1465       do k=1,1000
1466         if (ioverlap_last.eq.0) exit
1467
1468         do ires=1,ioverlap_last
1469           i=ioverlap(ires)
1470           iti=iabs(itype(i,1))
1471           if ((iti.ne.10).and.(molnum(i).ne.5).and.(iti.ne.ntyp1)) then
1472             nsi=0
1473             fail=.true.
1474             do while (fail.and.nsi.le.maxsi)
1475               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1476               nsi=nsi+1
1477             enddo
1478             if(fail) goto 999
1479           endif
1480         enddo
1481
1482         call chainbuild
1483         call overlap_sc_list(ioverlap,ioverlap_last)
1484 !        write (iout,*) 'Overlaping residues ',ioverlap_last,
1485 !     &           (ioverlap(j),j=1,ioverlap_last)
1486       enddo
1487
1488       if (k.le.1000.and.ioverlap_last.eq.0) then
1489         scfail=.false.
1490         if (had_overlaps) then
1491           write (iout,*) '#OVERLAPing all corrected after ',k,&
1492                ' random generation'
1493         endif
1494       else
1495         scfail=.true.
1496         write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1497         write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1498       endif
1499
1500       return
1501
1502  999  continue
1503       write (iout,'(a30,i5,a12,i4)') &
1504                      '#OVERLAP FAIL in gen_side after',maxsi,&
1505                      'iter for RES',i
1506       scfail=.true.
1507       return
1508       end subroutine overlap_sc
1509 !-----------------------------------------------------------------------------
1510       subroutine overlap_sc_list(ioverlap,ioverlap_last)
1511       use calc_data
1512 !      implicit real*8 (a-h,o-z)
1513 !      include 'DIMENSIONS'
1514 !      include 'COMMON.GEO'
1515 !      include 'COMMON.LOCAL'
1516 !      include 'COMMON.IOUNITS'
1517 !      include 'COMMON.CHAIN'
1518 !      include 'COMMON.INTERACT'
1519 !      include 'COMMON.FFIELD'
1520 !      include 'COMMON.VAR'
1521 !      include 'COMMON.CALC'
1522       logical :: fail
1523       integer,dimension(nres) :: ioverlap !(maxres)
1524       integer :: ioverlap_last
1525 !el local variables
1526       integer :: ind,iint
1527       real(kind=8) :: redfac,sig        !rrij,sigsq,
1528       integer :: itypi,itypj,itypi1
1529       real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1530       data redfac /0.5D0/
1531
1532       ioverlap_last=0
1533 ! Check for SC-SC overlaps and mark residues
1534 !      print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1535       ind=0
1536       do i=iatsc_s,iatsc_e
1537         if (itype(i,molnum(i)).eq.ntyp1_molec(molnum(i))) cycle
1538         if (molnum(i).eq.5) print *,"WTF",i,iatsc_s,iatsc_e
1539         if (molnum(i).eq.5) cycle
1540         itypi=iabs(itype(i,molnum(i)))
1541         itypi1=iabs(itype(i+1,1))
1542         xi=c(1,nres+i)
1543         yi=c(2,nres+i)
1544         zi=c(3,nres+i)
1545         dxi=dc_norm(1,nres+i)
1546         dyi=dc_norm(2,nres+i)
1547         dzi=dc_norm(3,nres+i)
1548         dsci_inv=dsc_inv(itypi)
1549 !
1550        do iint=1,nint_gr(i)
1551          do j=istart(i,iint),iend(i,iint)
1552          if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
1553             ind=ind+1
1554             itypj=iabs(itype(j,molnum(j)))
1555             dscj_inv=dsc_inv(itypj)
1556             sig0ij=sigma(itypi,itypj)
1557             chi1=chi(itypi,itypj)
1558             chi2=chi(itypj,itypi)
1559             chi12=chi1*chi2
1560             chip1=chip(itypi)
1561             chip2=chip(itypj)
1562             chip12=chip1*chip2
1563             alf1=alp(itypi)
1564             alf2=alp(itypj)
1565             alf12=0.5D0*(alf1+alf2)
1566           if (j.gt.i+1) then
1567            rcomp=sigmaii(itypi,itypj)
1568           else
1569            rcomp=sigma(itypi,itypj)
1570           endif
1571 !         print '(2(a3,2i3),a3,2f10.5)',
1572 !     &        ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1573 !     &        ,rcomp
1574             xj=c(1,nres+j)-xi
1575             yj=c(2,nres+j)-yi
1576             zj=c(3,nres+j)-zi
1577             dxj=dc_norm(1,nres+j)
1578             dyj=dc_norm(2,nres+j)
1579             dzj=dc_norm(3,nres+j)
1580             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1581             rij=dsqrt(rrij)
1582             call sc_angular
1583             sigsq=1.0D0/sigsq
1584             sig=sig0ij*dsqrt(sigsq)
1585             rij_shift=1.0D0/rij-sig+sig0ij
1586
1587 !t          if ( 1.0/rij .lt. redfac*rcomp .or.
1588 !t     &       rij_shift.le.0.0D0 ) then
1589             if ( rij_shift.le.0.0D0 ) then
1590 !d           write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1591 !d     &     'overlap SC-SC: i=',i,' j=',j,
1592 !d     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
1593 !d     &     rcomp,1.0/rij,rij_shift
1594           ioverlap_last=ioverlap_last+1
1595           ioverlap(ioverlap_last)=i
1596           do k=1,ioverlap_last-1
1597            if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1598           enddo
1599           ioverlap_last=ioverlap_last+1
1600           ioverlap(ioverlap_last)=j
1601           do k=1,ioverlap_last-1
1602            if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1603           enddo
1604          endif
1605         enddo
1606        enddo
1607       enddo
1608       return
1609       end subroutine overlap_sc_list
1610 #endif
1611 !-----------------------------------------------------------------------------
1612 ! energy_p_new_barrier.F
1613 !-----------------------------------------------------------------------------
1614       subroutine sc_angular
1615 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1616 ! om12. Called by ebp, egb, and egbv.
1617       use calc_data
1618 !      implicit none
1619 !      include 'COMMON.CALC'
1620 !      include 'COMMON.IOUNITS'
1621       erij(1)=xj*rij
1622       erij(2)=yj*rij
1623       erij(3)=zj*rij
1624       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1625       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1626       om12=dxi*dxj+dyi*dyj+dzi*dzj
1627       chiom12=chi12*om12
1628 ! Calculate eps1(om12) and its derivative in om12
1629       faceps1=1.0D0-om12*chiom12
1630       faceps1_inv=1.0D0/faceps1
1631       eps1=dsqrt(faceps1_inv)
1632 ! Following variable is eps1*deps1/dom12
1633       eps1_om12=faceps1_inv*chiom12
1634 ! diagnostics only
1635 !      faceps1_inv=om12
1636 !      eps1=om12
1637 !      eps1_om12=1.0d0
1638 !      write (iout,*) "om12",om12," eps1",eps1
1639 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1640 ! and om12.
1641       om1om2=om1*om2
1642       chiom1=chi1*om1
1643       chiom2=chi2*om2
1644       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1645       sigsq=1.0D0-facsig*faceps1_inv
1646       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1647       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1648       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1649 ! diagnostics only
1650 !      sigsq=1.0d0
1651 !      sigsq_om1=0.0d0
1652 !      sigsq_om2=0.0d0
1653 !      sigsq_om12=0.0d0
1654 !      write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1655 !      write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1656 !     &    " eps1",eps1
1657 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1658       chipom1=chip1*om1
1659       chipom2=chip2*om2
1660       chipom12=chip12*om12
1661       facp=1.0D0-om12*chipom12
1662       facp_inv=1.0D0/facp
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
1680       return
1681       end subroutine sc_angular
1682 !-----------------------------------------------------------------------------
1683 ! initialize_p.F
1684       subroutine sc_angular_nucl
1685 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1686 ! om12. Called by ebp, egb, and egbv.
1687 !      use calc_data
1688 !      implicit none
1689 !      include 'COMMON.CALC'
1690 !      include 'COMMON.IOUNITS'
1691       use comm_locel
1692       use calc_data_nucl
1693       erij(1)=xj*rij
1694       erij(2)=yj*rij
1695       erij(3)=zj*rij
1696       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1697       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1698       om12=dxi*dxj+dyi*dyj+dzi*dzj
1699       chiom12=chi12*om12
1700 ! Calculate eps1(om12) and its derivative in om12
1701       faceps1=1.0D0-om12*chiom12
1702       faceps1_inv=1.0D0/faceps1
1703       eps1=dsqrt(faceps1_inv)
1704 ! Following variable is eps1*deps1/dom12
1705       eps1_om12=faceps1_inv*chiom12
1706 ! diagnostics only
1707 !      faceps1_inv=om12
1708 !      eps1=om12
1709 !      eps1_om12=1.0d0
1710 !      write (iout,*) "om12",om12," eps1",eps1
1711 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1712 ! and om12.
1713       om1om2=om1*om2
1714       chiom1=chi1*om1
1715       chiom2=chi2*om2
1716       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1717       sigsq=1.0D0-facsig*faceps1_inv
1718       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1719       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1720       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1721       chipom1=chip1*om1
1722       chipom2=chip2*om2
1723       chipom12=chip12*om12
1724       facp=1.0D0-om12*chipom12
1725       facp_inv=1.0D0/facp
1726       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1727 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1728 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1729 ! Following variable is the square root of eps2
1730       eps2rt=1.0D0-facp1*facp_inv
1731 ! Following three variables are the derivatives of the square root of eps
1732 ! in om1, om2, and om12.
1733       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1734       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1735       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1736 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1737       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1738 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1739 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1740 !     &  " eps2rt_om12",eps2rt_om12
1741 ! Calculate whole angle-dependent part of epsilon and contributions
1742 ! to its derivatives
1743       return
1744       end subroutine sc_angular_nucl
1745
1746 !-----------------------------------------------------------------------------
1747       subroutine int_bounds(total_ints,lower_bound,upper_bound)
1748 !      implicit real*8 (a-h,o-z)
1749 !      include 'DIMENSIONS'
1750       include 'mpif.h'
1751 !      include 'COMMON.SETUP'
1752       integer :: total_ints,lower_bound,upper_bound,nint
1753       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1754       integer :: i,nexcess
1755       nint=total_ints/nfgtasks
1756       do i=1,nfgtasks
1757         int4proc(i-1)=nint
1758       enddo
1759       nexcess=total_ints-nint*nfgtasks
1760       do i=1,nexcess
1761         int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1762       enddo
1763       lower_bound=0
1764       do i=0,fg_rank-1
1765         lower_bound=lower_bound+int4proc(i)
1766       enddo
1767       upper_bound=lower_bound+int4proc(fg_rank)
1768       lower_bound=lower_bound+1
1769       return
1770       end subroutine int_bounds
1771 !-----------------------------------------------------------------------------
1772       subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1773 !      implicit real*8 (a-h,o-z)
1774 !      include 'DIMENSIONS'
1775       include 'mpif.h'
1776 !      include 'COMMON.SETUP'
1777       integer :: total_ints,lower_bound,upper_bound,nint
1778       integer :: nexcess,i
1779       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1780       nint=total_ints/nfgtasks1
1781       do i=1,nfgtasks1
1782         int4proc(i-1)=nint
1783       enddo
1784       nexcess=total_ints-nint*nfgtasks1
1785       do i=1,nexcess
1786         int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1787       enddo
1788       lower_bound=0
1789       do i=0,fg_rank1-1
1790         lower_bound=lower_bound+int4proc(i)
1791       enddo
1792       upper_bound=lower_bound+int4proc(fg_rank1)
1793       lower_bound=lower_bound+1
1794       return
1795       end subroutine int_bounds1
1796 !-----------------------------------------------------------------------------
1797 ! intcartderiv.F
1798 !-----------------------------------------------------------------------------
1799       subroutine chainbuild_cart
1800 !      implicit real*8 (a-h,o-z)
1801 !      include 'DIMENSIONS'
1802       use control_data
1803 #ifdef MPI
1804       include 'mpif.h'
1805 #endif
1806 !      include 'COMMON.SETUP'
1807 !      include 'COMMON.CHAIN'
1808 !      include 'COMMON.LOCAL'
1809 !      include 'COMMON.TIME1'
1810 !      include 'COMMON.IOUNITS'
1811       integer :: j,i,ierror,ierr
1812       real(kind=8) :: time00,time01
1813 #ifdef MPI
1814       if (nfgtasks.gt.1) then
1815 !        write (iout,*) "BCAST in chainbuild_cart"
1816 !        call flush(iout)
1817 ! Broadcast the order to build the chain and compute internal coordinates
1818 ! to the slaves. The slaves receive the order in ERGASTULUM.
1819         time00=MPI_Wtime()
1820 !      write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1821 !      do i=0,nres
1822 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1823 !     &   (dc(j,i+nres),j=1,3)
1824 !      enddo
1825         if (fg_rank.eq.0) &
1826           call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1827         time_bcast7=time_bcast7+MPI_Wtime()-time00
1828         time01=MPI_Wtime()
1829         call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1830           king,FG_COMM,IERR)
1831 !      write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1832 !      do i=0,nres
1833 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1834 !     &   (dc(j,i+nres),j=1,3)
1835 !      enddo
1836 !        write (iout,*) "End BCAST in chainbuild_cart"
1837 !        call flush(iout)
1838         time_bcast=time_bcast+MPI_Wtime()-time00
1839         time_bcastc=time_bcastc+MPI_Wtime()-time01
1840       endif
1841 #endif
1842       do j=1,3
1843         c(j,1)=dc(j,0)
1844       enddo
1845       do i=2,nres
1846         do j=1,3
1847           c(j,i)=c(j,i-1)+dc(j,i-1)
1848         enddo
1849       enddo
1850       do i=1,nres
1851         do j=1,3
1852           c(j,i+nres)=c(j,i)+dc(j,i+nres)
1853         enddo
1854       enddo
1855 !      write (iout,*) "CHAINBUILD_CART"
1856 !      call cartprint
1857       call int_from_cart1(.false.)
1858       return
1859       end subroutine chainbuild_cart
1860 !-----------------------------------------------------------------------------
1861 ! intcor.f
1862 !-----------------------------------------------------------------------------
1863       real(kind=8) function alpha(i1,i2,i3)
1864 !
1865 !  Calculates the planar angle between atoms (i1), (i2), and (i3).
1866 !
1867 !      implicit real*8 (a-h,o-z)
1868 !      include 'DIMENSIONS'
1869 !      include 'COMMON.GEO'
1870 !      include 'COMMON.CHAIN'
1871 !el local variables
1872       integer :: i1,i2,i3
1873       real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1874       x12=c(1,i1)-c(1,i2)
1875       x23=c(1,i3)-c(1,i2)
1876       y12=c(2,i1)-c(2,i2)
1877       y23=c(2,i3)-c(2,i2)
1878       z12=c(3,i1)-c(3,i2)
1879       z23=c(3,i3)-c(3,i2)
1880       vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1881       wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1882       scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1883       alpha=arcos(scalar)
1884       return
1885       end function alpha
1886 !-----------------------------------------------------------------------------
1887       real(kind=8) function beta(i1,i2,i3,i4)
1888 !
1889 !  Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1890 !
1891 !      implicit real*8 (a-h,o-z)
1892 !      include 'DIMENSIONS'
1893 !      include 'COMMON.GEO'
1894 !      include 'COMMON.CHAIN'
1895 !el local variables
1896       integer :: i1,i2,i3,i4
1897       real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1898       real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1899       real(kind=8) :: tx,ty,tz
1900       x12=c(1,i1)-c(1,i2)
1901       x23=c(1,i3)-c(1,i2)
1902       x34=c(1,i4)-c(1,i3)
1903       y12=c(2,i1)-c(2,i2)
1904       y23=c(2,i3)-c(2,i2)
1905       y34=c(2,i4)-c(2,i3)
1906       z12=c(3,i1)-c(3,i2)
1907       z23=c(3,i3)-c(3,i2)
1908       z34=c(3,i4)-c(3,i3)
1909 !d    print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1910 !d    print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1911 !d    print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1912       wx=-y23*z34+y34*z23
1913       wy=x23*z34-z23*x34
1914       wz=-x23*y34+y23*x34
1915       wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1916       vx=y12*z23-z12*y23
1917       vy=-x12*z23+z12*x23
1918       vz=x12*y23-y12*x23
1919       vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1920       if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1921       scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1922       if (dabs(scalar).gt.1.0D0) &
1923       scalar=0.99999999999999D0*scalar/dabs(scalar)
1924       angle=dacos(scalar)
1925 !d    print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1926 !d   &scalar,angle
1927       else
1928       angle=pi
1929       endif
1930 !     if (angle.le.0.0D0) angle=pi+angle
1931       tx=vy*wz-vz*wy
1932       ty=-vx*wz+vz*wx
1933       tz=vx*wy-vy*wx
1934       scalar=tx*x23+ty*y23+tz*z23
1935       if (scalar.lt.0.0D0) angle=-angle
1936       beta=angle
1937       return
1938       end function beta
1939 !-----------------------------------------------------------------------------
1940       real(kind=8) function dist(i1,i2)
1941 !
1942 !  Calculates the distance between atoms (i1) and (i2).
1943 !
1944 !      implicit real*8 (a-h,o-z)
1945 !      include 'DIMENSIONS'
1946 !      include 'COMMON.GEO'
1947 !      include 'COMMON.CHAIN'
1948 !el local variables
1949       integer :: i1,i2
1950       real(kind=8) :: x12,y12,z12
1951       x12=c(1,i1)-c(1,i2)
1952       y12=c(2,i1)-c(2,i2)
1953       z12=c(3,i1)-c(3,i2)
1954       dist=dsqrt(x12*x12+y12*y12+z12*z12)
1955       return
1956       end function dist
1957 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1958 !-----------------------------------------------------------------------------
1959 ! local_move.f
1960 !-----------------------------------------------------------------------------
1961       subroutine local_move_init(debug)
1962 !rc      implicit none
1963
1964 !     Includes
1965 !      implicit real*8 (a-h,o-z)
1966 !      include 'DIMENSIONS'  ! Needed by COMMON.LOCAL
1967 !      include 'COMMON.GEO'  ! For pi, deg2rad
1968 !      include 'COMMON.LOCAL'  ! For vbl
1969 !      include 'COMMON.LOCMOVE'
1970
1971 !     INPUT arguments
1972       logical :: debug
1973
1974
1975 !     Determine wheter to do some debugging output
1976       locmove_output=debug
1977
1978 !     Set the init_called flag to 1
1979       init_called=1
1980
1981 !     The following are never changed
1982       min_theta=60.D0*deg2rad  ! (0,PI)
1983       max_theta=175.D0*deg2rad  ! (0,PI)
1984       dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1985       dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1986       flag=1.0D300
1987       small=1.0D-5
1988       small2=0.5*small*small
1989
1990 !     Not really necessary...
1991       a_n=0
1992       b_n=0
1993       res_n=0
1994
1995       return
1996       end subroutine local_move_init
1997 !-----------------------------------------------------------------------------
1998       subroutine local_move(n_start, n_end, PHImin, PHImax)
1999 !     Perform a local move between residues m and n (inclusive)
2000 !     PHImin and PHImax [0,PI] determine the size of the move
2001 !     Works on whatever structure is in the variables theta and phi,
2002 !     sidechain variables are left untouched
2003 !     The final structure is NOT minimized, but both the cartesian
2004 !     variables c and the angles are up-to-date at the end (no further
2005 !     chainbuild is required)
2006 !rc      implicit none
2007       use random,only:ran_number
2008 !     Includes
2009 !      implicit real*8 (a-h,o-z)
2010 !      include 'DIMENSIONS'
2011 !      include 'COMMON.GEO'
2012 !      include 'COMMON.CHAIN'
2013 !      include 'COMMON.VAR'
2014 !      include 'COMMON.MINIM'
2015 !      include 'COMMON.SBRIDGE'
2016 !      include 'COMMON.LOCMOVE'
2017
2018 !     External functions
2019 !EL      integer move_res
2020 !EL      external move_res
2021 !EL      double precision ran_number
2022 !EL      external ran_number
2023
2024 !     INPUT arguments
2025       integer :: n_start, n_end  ! First and last residues to move
2026       real(kind=8) :: PHImin, PHImax  ! min/max angles [0,PI]
2027
2028 !     Local variables
2029       integer :: i,j
2030       real(kind=8) :: min,max
2031       integer :: iretcode
2032
2033
2034 !     Check if local_move_init was called.  This assumes that it
2035 !     would not be 1 if not explicitely initialized
2036       if (init_called.ne.1) then
2037         write(6,*)'   ***   local_move_init not called!!!'
2038         stop
2039       endif
2040
2041 !     Quick check for crazy range
2042       if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2043         write(6,'(a,i3,a,i3)') &
2044              '   ***   Cannot make local move between n_start = ',&
2045              n_start,' and n_end = ',n_end
2046         return
2047       endif
2048
2049 !     Take care of end residues first...
2050       if (n_start.eq.1) then
2051 !     Move residue 1 (completely random)
2052         theta(3)=ran_number(min_theta,max_theta)
2053         phi(4)=ran_number(-PI,PI)
2054         i=2
2055       else
2056         i=n_start
2057       endif
2058       if (n_end.eq.nres) then
2059 !     Move residue nres (completely random)
2060         theta(nres)=ran_number(min_theta,max_theta)
2061         phi(nres)=ran_number(-PI,PI)
2062         j=nres-1
2063       else
2064         j=n_end
2065       endif
2066
2067 !     ...then go through all other residues one by one
2068 !     Start from the two extremes and converge
2069       call chainbuild
2070       do while (i.le.j)
2071         min=PHImin
2072         max=PHImax
2073 !$$$c     Move the first two residues by less than the others
2074 !$$$        if (i-n_start.lt.3) then
2075 !$$$          if (i-n_start.eq.0) then
2076 !$$$            min=0.4*PHImin
2077 !$$$            max=0.4*PHImax
2078 !$$$          else if (i-n_start.eq.1) then
2079 !$$$            min=0.8*PHImin
2080 !$$$            max=0.8*PHImax
2081 !$$$          else if (i-n_start.eq.2) then
2082 !$$$            min=PHImin
2083 !$$$            max=PHImax
2084 !$$$          endif
2085 !$$$        endif
2086
2087 !     The actual move, on residue i
2088         iretcode=move_res(min,max,i)  ! Discard iretcode
2089         i=i+1
2090
2091         if (i.le.j) then
2092           min=PHImin
2093           max=PHImax
2094 !$$$c     Move the last two residues by less than the others
2095 !$$$          if (n_end-j.lt.3) then
2096 !$$$            if (n_end-j.eq.0) then
2097 !$$$              min=0.4*PHImin
2098 !$$$              max=0.4*PHImax
2099 !$$$            else if (n_end-j.eq.1) then
2100 !$$$              min=0.8*PHImin
2101 !$$$              max=0.8*PHImax
2102 !$$$            else if (n_end-j.eq.2) then
2103 !$$$              min=PHImin
2104 !$$$              max=PHImax
2105 !$$$            endif
2106 !$$$          endif
2107
2108 !     The actual move, on residue j
2109           iretcode=move_res(min,max,j)  ! Discard iretcode
2110           j=j-1
2111         endif
2112       enddo
2113
2114       call int_from_cart(.false.,.false.)
2115
2116       return
2117       end subroutine local_move
2118 !-----------------------------------------------------------------------------
2119       subroutine output_tabs
2120 !     Prints out the contents of a_..., b_..., res_...
2121 !      implicit none
2122
2123 !     Includes
2124 !      include 'COMMON.GEO'
2125 !      include 'COMMON.LOCMOVE'
2126
2127 !     Local variables
2128       integer :: i,j
2129
2130       write(6,*)'a_...'
2131       write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2132       write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2133
2134       write(6,*)'b_...'
2135       write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2136       write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2137
2138       write(6,*)'res_...'
2139       write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2140       write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2141       write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2142       write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2143
2144       return
2145       end subroutine output_tabs
2146 !-----------------------------------------------------------------------------
2147       subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2148 !     Only uses angles if [0,PI] (but PHImin cannot be 0.,
2149 !     and PHImax cannot be PI)
2150 !      implicit none
2151
2152 !     Includes
2153 !      include 'COMMON.GEO'
2154
2155 !     INPUT arguments
2156       real(kind=8) :: PHImin,PHImax
2157
2158 !     OUTPUT arguments
2159       integer :: n
2160       real(kind=8),dimension(0:3) :: ang
2161       logical,dimension(0:2,0:3) :: tab
2162
2163
2164       if (PHImin .eq. PHImax) then
2165 !     Special case with two 010's
2166         n = 2;
2167         ang(0) = -PHImin;
2168         ang(1) = PHImin;
2169         tab(0,0) = .false.
2170         tab(2,0) = .false.
2171         tab(0,1) = .false.
2172         tab(2,1) = .false.
2173         tab(1,0) = .true.
2174         tab(1,1) = .true.
2175       else if (PHImin .eq. PI) then
2176 !     Special case with one 010
2177         n = 1
2178         ang(0) = PI
2179         tab(0,0) = .false.
2180         tab(2,0) = .false.
2181         tab(1,0) = .true.
2182       else if (PHImax .eq. 0.) then
2183 !     Special case with one 010
2184         n = 1
2185         ang(0) = 0.
2186         tab(0,0) = .false.
2187         tab(2,0) = .false.
2188         tab(1,0) = .true.
2189       else
2190 !     Standard cases
2191         n = 0
2192         if (PHImin .gt. 0.) then
2193 !     Start of range (011)
2194           ang(n) = PHImin
2195           tab(0,n) = .false.
2196           tab(1,n) = .true.
2197           tab(2,n) = .true.
2198 !     End of range (110)
2199           ang(n+1) = -PHImin
2200           tab(0,n+1) = .true.
2201           tab(1,n+1) = .true.
2202           tab(2,n+1) = .false.
2203           n = n+2
2204         endif
2205         if (PHImax .lt. PI) then
2206 !     Start of range (011)
2207           ang(n) = -PHImax
2208           tab(0,n) = .false.
2209           tab(1,n) = .true.
2210           tab(2,n) = .true.
2211 !     End of range (110)
2212           ang(n+1) = PHImax
2213           tab(0,n+1) = .true.
2214           tab(1,n+1) = .true.
2215           tab(2,n+1) = .false.
2216           n = n+2
2217         endif
2218       endif
2219
2220       return
2221       end subroutine angles2tab
2222 !-----------------------------------------------------------------------------
2223       subroutine minmax_angles(x,y,z,r,n,ang,tab)
2224 !     When solutions do not exist, assume all angles
2225 !     are acceptable - i.e., initial geometry must be correct
2226 !      implicit none
2227
2228 !     Includes
2229 !      include 'COMMON.GEO'
2230 !      include 'COMMON.LOCMOVE'
2231
2232 !     Input arguments
2233       real(kind=8) :: x,y,z,r
2234
2235 !     Output arguments
2236       integer :: n
2237       real(kind=8),dimension(0:3) :: ang
2238       logical,dimension(0:2,0:3) :: tab
2239
2240 !     Local variables
2241       real(kind=8) :: num, denom, phi
2242       real(kind=8) :: Kmin, Kmax
2243       integer :: i
2244
2245
2246       num = x*x + y*y + z*z
2247       denom = x*x + y*y
2248       n = 0
2249       if (denom .gt. 0.) then
2250         phi = atan2(y,x)
2251         denom = 2.*r*sqrt(denom)
2252         num = num+r*r
2253         Kmin = (num - dmin2)/denom
2254         Kmax = (num - dmax2)/denom
2255
2256 !     Allowed values of K (else all angles are acceptable)
2257 !     -1 <= Kmin <  1
2258 !     -1 <  Kmax <= 1
2259         if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2260           Kmin = -flag
2261         else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2262           Kmin = PI
2263         else
2264           Kmin = acos(Kmin)
2265         endif
2266
2267         if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2268           Kmax = flag
2269         else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2270           Kmax = 0.
2271         else
2272           Kmax = acos(Kmax)
2273         endif
2274
2275         if (Kmax .lt. Kmin) Kmax = Kmin
2276
2277         call angles2tab(Kmin, Kmax, n, ang, tab)
2278
2279 !     Add phi and check that angles are within range (-PI,PI]
2280         do i=0,n-1
2281           ang(i) = ang(i)+phi
2282           if (ang(i) .le. -PI) then
2283             ang(i) = ang(i)+2.*PI
2284           else if (ang(i) .gt. PI) then
2285             ang(i) = ang(i)-2.*PI
2286           endif
2287         enddo
2288       endif
2289
2290       return
2291       end subroutine minmax_angles
2292 !-----------------------------------------------------------------------------
2293       subroutine construct_tab
2294 !     Take a_... and b_... values and produces the results res_...
2295 !     x_ang are assumed to be all different (diff > small)
2296 !     x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2297 !      implicit none
2298
2299 !     Includes
2300 !      include 'COMMON.LOCMOVE'
2301
2302 !     Local variables
2303       integer :: n_max,i,j,index
2304       logical :: done
2305       real(kind=8) :: phi
2306
2307
2308       n_max = a_n + b_n
2309       if (n_max .eq. 0) then
2310         res_n = 0
2311         return
2312       endif
2313
2314       do i=0,n_max-1
2315         do j=0,1
2316           res_tab(j,0,i) = .true.
2317           res_tab(j,2,i) = .true.
2318           res_tab(j,1,i) = .false.
2319         enddo
2320       enddo
2321
2322       index = 0
2323       phi = -flag
2324       done = .false.
2325       do while (.not.done)
2326         res_ang(index) = flag
2327
2328 !     Check a first...
2329         do i=0,a_n-1
2330           if ((a_ang(i)-phi).gt.small .and. &
2331                a_ang(i) .lt. res_ang(index)) then
2332 !     Found a lower angle
2333             res_ang(index) = a_ang(i)
2334 !     Copy the values from a_tab into res_tab(0,,)
2335             res_tab(0,0,index) = a_tab(0,i)
2336             res_tab(0,1,index) = a_tab(1,i)
2337             res_tab(0,2,index) = a_tab(2,i)
2338 !     Set default values for res_tab(1,,)
2339             res_tab(1,0,index) = .true.
2340             res_tab(1,1,index) = .false.
2341             res_tab(1,2,index) = .true.
2342           else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2343 !     Found an equal angle (can only be equal to a b_ang)
2344             res_tab(0,0,index) = a_tab(0,i)
2345             res_tab(0,1,index) = a_tab(1,i)
2346             res_tab(0,2,index) = a_tab(2,i)
2347           endif
2348         enddo
2349 !     ...then check b
2350         do i=0,b_n-1
2351           if ((b_ang(i)-phi).gt.small .and. &
2352                b_ang(i) .lt. res_ang(index)) then
2353 !     Found a lower angle
2354             res_ang(index) = b_ang(i)
2355 !     Copy the values from b_tab into res_tab(1,,)
2356             res_tab(1,0,index) = b_tab(0,i)
2357             res_tab(1,1,index) = b_tab(1,i)
2358             res_tab(1,2,index) = b_tab(2,i)
2359 !     Set default values for res_tab(0,,)
2360             res_tab(0,0,index) = .true.
2361             res_tab(0,1,index) = .false.
2362             res_tab(0,2,index) = .true.
2363           else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2364 !     Found an equal angle (can only be equal to an a_ang)
2365             res_tab(1,0,index) = b_tab(0,i)
2366             res_tab(1,1,index) = b_tab(1,i)
2367             res_tab(1,2,index) = b_tab(2,i)
2368           endif
2369         enddo
2370
2371         if (res_ang(index) .eq. flag) then
2372           res_n = index
2373           done = .true.
2374         else if (index .eq. n_max-1) then
2375           res_n = n_max
2376           done = .true.
2377         else
2378           phi = res_ang(index)  ! Store previous angle
2379           index = index+1
2380         endif
2381       enddo
2382
2383 !     Fill the gaps
2384 !     First a...
2385       index = 0
2386       if (a_n .gt. 0) then
2387         do while (.not.res_tab(0,1,index))
2388           index=index+1
2389         enddo
2390         done = res_tab(0,2,index)
2391         do i=index+1,res_n-1
2392           if (res_tab(0,1,i)) then
2393             done = res_tab(0,2,i)
2394           else
2395             res_tab(0,0,i) = done
2396             res_tab(0,1,i) = done
2397             res_tab(0,2,i) = done
2398           endif
2399         enddo
2400         done = res_tab(0,0,index)
2401         do i=index-1,0,-1
2402           if (res_tab(0,1,i)) then
2403             done = res_tab(0,0,i)
2404           else
2405             res_tab(0,0,i) = done
2406             res_tab(0,1,i) = done
2407             res_tab(0,2,i) = done
2408           endif
2409         enddo
2410       else
2411         do i=0,res_n-1
2412           res_tab(0,0,i) = .true.
2413           res_tab(0,1,i) = .true.
2414           res_tab(0,2,i) = .true.
2415         enddo
2416       endif
2417 !     ...then b
2418       index = 0
2419       if (b_n .gt. 0) then
2420         do while (.not.res_tab(1,1,index))
2421           index=index+1
2422         enddo
2423         done = res_tab(1,2,index)
2424         do i=index+1,res_n-1
2425           if (res_tab(1,1,i)) then
2426             done = res_tab(1,2,i)
2427           else
2428             res_tab(1,0,i) = done
2429             res_tab(1,1,i) = done
2430             res_tab(1,2,i) = done
2431           endif
2432         enddo
2433         done = res_tab(1,0,index)
2434         do i=index-1,0,-1
2435           if (res_tab(1,1,i)) then
2436             done = res_tab(1,0,i)
2437           else
2438             res_tab(1,0,i) = done
2439             res_tab(1,1,i) = done
2440             res_tab(1,2,i) = done
2441           endif
2442         enddo
2443       else
2444         do i=0,res_n-1
2445           res_tab(1,0,i) = .true.
2446           res_tab(1,1,i) = .true.
2447           res_tab(1,2,i) = .true.
2448         enddo
2449       endif
2450
2451 !     Finally fill the last row with AND operation
2452       do i=0,res_n-1
2453         do j=0,2
2454           res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2455         enddo
2456       enddo
2457
2458       return
2459       end subroutine construct_tab
2460 !-----------------------------------------------------------------------------
2461       subroutine construct_ranges(phi_n,phi_start,phi_end)
2462 !     Given the data in res_..., construct a table of
2463 !     min/max allowed angles
2464 !      implicit none
2465
2466 !     Includes
2467 !      include 'COMMON.GEO'
2468 !      include 'COMMON.LOCMOVE'
2469
2470 !     Output arguments
2471       integer :: phi_n
2472       real(kind=8),dimension(0:11) :: phi_start,phi_end
2473
2474 !     Local variables
2475       logical :: done
2476       integer :: index
2477
2478
2479       if (res_n .eq. 0) then
2480 !     Any move is allowed
2481         phi_n = 1
2482         phi_start(0) = -PI
2483         phi_end(0) = PI
2484       else
2485         phi_n = 0
2486         index = 0
2487         done = .false.
2488         do while (.not.done)
2489 !     Find start of range (01x)
2490           done = .false.
2491           do while (.not.done)
2492             if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2493               index=index+1
2494             else
2495               done = .true.
2496               phi_start(phi_n) = res_ang(index)
2497             endif
2498             if (index .eq. res_n) done = .true.
2499           enddo
2500 !     If a start was found (index < res_n), find the end of range (x10)
2501 !     It may not be found without wrapping around
2502           if (index .lt. res_n) then
2503             done = .false.
2504             do while (.not.done)
2505               if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2506                 index=index+1
2507               else
2508                 done = .true.
2509               endif
2510               if (index .eq. res_n) done = .true.
2511             enddo
2512             if (index .lt. res_n) then
2513 !     Found the end of the range
2514               phi_end(phi_n) = res_ang(index)
2515               phi_n=phi_n+1
2516               index=index+1
2517               if (index .eq. res_n) then
2518                 done = .true.
2519               else
2520                 done = .false.
2521               endif
2522             else
2523 !     Need to wrap around
2524               done = .true.
2525               phi_end(phi_n) = flag
2526             endif
2527           endif
2528         enddo
2529 !     Take care of the last one if need to wrap around
2530         if (phi_end(phi_n) .eq. flag) then
2531           index = 0
2532           do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2533             index=index+1
2534           enddo
2535           phi_end(phi_n) = res_ang(index) + 2.*PI
2536           phi_n=phi_n+1
2537         endif
2538       endif
2539
2540       return
2541       end subroutine construct_ranges
2542 !-----------------------------------------------------------------------------
2543       subroutine fix_no_moves(phi)
2544 !      implicit none
2545
2546 !     Includes
2547 !      include 'COMMON.GEO'
2548 !      include 'COMMON.LOCMOVE'
2549
2550 !     Output arguments
2551       real(kind=8) :: phi
2552
2553 !     Local variables
2554       integer :: index
2555       real(kind=8) :: diff,temp
2556
2557
2558 !     Look for first 01x in gammas (there MUST be at least one)
2559       diff = flag
2560       index = 0
2561       do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2562         index=index+1
2563       enddo
2564       if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2565 !     Try to increase PHImax
2566         if (index .gt. 0) then
2567           phi = res_ang(index-1)
2568           diff = abs(res_ang(index) - res_ang(index-1))
2569         endif
2570 !     Look for last (corresponding) x10
2571         index = res_n - 1
2572         do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2573           index=index-1
2574         enddo
2575         if (index .lt. res_n-1) then
2576           temp = abs(res_ang(index) - res_ang(index+1))
2577           if (temp .lt. diff) then
2578             phi = res_ang(index+1)
2579             diff = temp
2580           endif
2581         endif
2582       endif
2583
2584 !     If increasing PHImax didn't work, decreasing PHImin
2585 !     will (with one exception)
2586 !     Look for first x10 (there MUST be at least one)
2587       index = 0
2588       do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2589         index=index+1
2590       enddo
2591       if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2592 !     Try to decrease PHImin
2593         if (index .lt. res_n-1) then
2594           temp = abs(res_ang(index) - res_ang(index+1))
2595           if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2596             phi = res_ang(index+1)
2597             diff = temp
2598           endif
2599         endif
2600 !     Look for last (corresponding) 01x
2601         index = res_n - 1
2602         do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2603           index=index-1
2604         enddo
2605         if (index .gt. 0) then
2606           temp = abs(res_ang(index) - res_ang(index-1))
2607           if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2608             phi = res_ang(index-1)
2609             diff = temp
2610           endif
2611         endif
2612       endif
2613
2614 !     If it still didn't work, it must be PHImax == 0. or PHImin == PI
2615       if (diff .eq. flag) then
2616         index = 0
2617         if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2618              res_tab(index,1,2)) index = res_n - 1
2619 !     This MUST work at this point
2620         if (index .eq. 0) then
2621           phi = res_ang(1)
2622         else
2623           phi = res_ang(index - 1)
2624         endif
2625       endif
2626
2627       return
2628       end subroutine fix_no_moves
2629 !-----------------------------------------------------------------------------
2630       integer function move_res(PHImin,PHImax,i_move)
2631 !     Moves residue i_move (in array c), leaving everything else fixed
2632 !     Starting geometry is not checked, it should be correct!
2633 !     R(,i_move) is the only residue that will move, but must have
2634 !     1 < i_move < nres (i.e., cannot move ends)
2635 !     Whether any output is done is controlled by locmove_output
2636 !rc      implicit none
2637       use random,only:ran_number
2638 !     Includes
2639 !      implicit real*8 (a-h,o-z)
2640 !      include 'DIMENSIONS'
2641 !      include 'COMMON.CHAIN'
2642 !      include 'COMMON.GEO'
2643 !      include 'COMMON.LOCMOVE'
2644
2645 !     External functions
2646 !EL      double precision ran_number
2647 !EL      external ran_number
2648
2649 !     Input arguments
2650       real(kind=8) :: PHImin,PHImax
2651       integer :: i_move
2652
2653 !     RETURN VALUES:
2654 !     0: move successfull
2655 !     1: Dmin or Dmax had to be modified
2656 !     2: move failed - check your input geometry
2657
2658
2659 !     Local variables
2660       real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2661       real(kind=8),dimension(0:2) :: P
2662       logical :: no_moves,done
2663       integer :: index,i,j
2664       real(kind=8) :: phi,temp,radius
2665       real(kind=8),dimension(0:11) :: phi_start,phi_end
2666       integer :: phi_n
2667
2668 !     Set up the coordinate system
2669       do i=0,2
2670         Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2671       enddo
2672
2673       do i=0,2
2674         Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2675       enddo
2676       temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2677       do i=0,2
2678         Z(i)=Z(i)/temp
2679       enddo
2680
2681       do i=0,2
2682         X(i)=c(i+1,i_move)-Orig(i)
2683       enddo
2684 !     radius is the radius of the circle on which c(,i_move) can move
2685       radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2686       do i=0,2
2687         X(i)=X(i)/radius
2688       enddo
2689
2690       Y(0)=Z(1)*X(2)-X(1)*Z(2)
2691       Y(1)=X(0)*Z(2)-Z(0)*X(2)
2692       Y(2)=Z(0)*X(1)-X(0)*Z(1)
2693
2694 !     Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2695       if (i_move.gt.2) then
2696         do i=0,2
2697           P(i)=c(i+1,i_move-2)-Orig(i)
2698         enddo
2699         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2700              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2701              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2702              radius,a_n,a_ang,a_tab)
2703       else
2704         a_n=0
2705       endif
2706
2707 !     Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2708       if (i_move.lt.nres-2) then
2709         do i=0,2
2710           P(i)=c(i+1,i_move+2)-Orig(i)
2711         enddo
2712         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2713              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2714              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2715              radius,b_n,b_ang,b_tab)
2716       else
2717         b_n=0
2718       endif
2719
2720 !     Construct the resulting table for alpha and beta
2721       call construct_tab()
2722
2723       if (locmove_output) then
2724         print *,'ALPHAS & BETAS TABLE'
2725         call output_tabs()
2726       endif
2727
2728 !     Check that there is at least one possible move
2729       no_moves = .true.
2730       if (res_n .eq. 0) then
2731         no_moves = .false.
2732       else
2733         index = 0
2734         do while ((index .lt. res_n) .and. no_moves)
2735           if (res_tab(2,1,index)) no_moves = .false.
2736           index=index+1
2737         enddo
2738       endif
2739       if (no_moves) then
2740         if (locmove_output) print *,'   ***   Cannot move anywhere'
2741         move_res=2
2742         return
2743       endif
2744
2745 !     Transfer res_... into a_...
2746       a_n = 0
2747       do i=0,res_n-1
2748         if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2749              (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2750           a_ang(a_n) = res_ang(i)
2751           do j=0,2
2752             a_tab(j,a_n) = res_tab(2,j,i)
2753           enddo
2754           a_n=a_n+1
2755         endif
2756       enddo
2757
2758 !     Check that the PHI's are within [0,PI]
2759       if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2760       if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2761       if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2762       if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2763       if (PHImax .lt. PHImin) PHImax = PHImin
2764 !     Calculate min and max angles coming from PHImin and PHImax,
2765 !     and put them in b_...
2766       call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2767 !     Construct the final table
2768       call construct_tab()
2769
2770       if (locmove_output) then
2771         print *,'FINAL TABLE'
2772         call output_tabs()
2773       endif
2774
2775 !     Check that there is at least one possible move
2776       no_moves = .true.
2777       if (res_n .eq. 0) then
2778         no_moves = .false.
2779       else
2780         index = 0
2781         do while ((index .lt. res_n) .and. no_moves)
2782           if (res_tab(2,1,index)) no_moves = .false.
2783           index=index+1
2784         enddo
2785       endif
2786
2787       if (no_moves) then
2788 !     Take care of the case where no solution exists...
2789         call fix_no_moves(phi)
2790         if (locmove_output) then
2791           print *,'   ***   Had to modify PHImin or PHImax'
2792           print *,'phi: ',phi*rad2deg
2793         endif
2794         move_res=1
2795       else
2796 !     ...or calculate the solution
2797 !     Construct phi_start/phi_end arrays
2798         call construct_ranges(phi_n, phi_start, phi_end)
2799 !     Choose random angle phi in allowed range(s)
2800         temp = 0.
2801         do i=0,phi_n-1
2802           temp = temp + phi_end(i) - phi_start(i)
2803         enddo
2804         phi = ran_number(phi_start(0),phi_start(0)+temp)
2805         index = 0
2806         done = .false.
2807         do while (.not.done)
2808           if (phi .lt. phi_end(index)) then
2809             done = .true.
2810           else
2811             index=index+1
2812           endif
2813           if (index .eq. phi_n) then
2814             done = .true.
2815           else if (.not.done) then
2816             phi = phi + phi_start(index) - phi_end(index-1)
2817           endif
2818         enddo
2819         if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2820         if (phi .gt. PI) phi = phi-2.*PI
2821
2822         if (locmove_output) then
2823           print *,'ALLOWED RANGE(S)'
2824           do i=0,phi_n-1
2825             print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2826           enddo
2827           print *,'phi: ',phi*rad2deg
2828         endif
2829         move_res=0
2830       endif
2831
2832 !     Re-use radius as temp variable
2833       temp=radius*cos(phi)
2834       radius=radius*sin(phi)
2835       do i=0,2
2836         c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2837       enddo
2838
2839       return
2840       end function move_res
2841 !-----------------------------------------------------------------------------
2842       subroutine loc_test
2843 !rc      implicit none
2844
2845 !     Includes
2846 !      implicit real*8 (a-h,o-z)
2847 !      include 'DIMENSIONS'
2848 !      include 'COMMON.GEO'
2849 !      include 'COMMON.LOCAL'
2850 !      include 'COMMON.LOCMOVE'
2851
2852 !     External functions
2853 !EL      integer move_res
2854 !EL      external move_res
2855
2856 !     Local variables
2857       integer :: i,j,imov
2858       integer :: phi_n
2859       real(kind=8),dimension(0:11) :: phi_start,phi_end
2860       real(kind=8) :: phi
2861       real(kind=8),dimension(0:2,0:5) :: R
2862
2863       locmove_output=.true.
2864
2865 !      call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2866 !      call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2867 !      call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2868 !      call construct_tab
2869 !      call output_tabs
2870
2871 !      call construct_ranges(phi_n,phi_start,phi_end)
2872 !      do i=0,phi_n-1
2873 !        print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2874 !      enddo
2875
2876 !      call fix_no_moves(phi)
2877 !      print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2878
2879       R(0,0)=0.D0
2880       R(1,0)=0.D0
2881       R(2,0)=0.D0
2882       R(0,1)=0.D0
2883       R(1,1)=-cos(28.D0*deg2rad)
2884       R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2885       R(0,2)=0.D0
2886       R(1,2)=0.D0
2887       R(2,2)=-0.5D0
2888       R(0,3)=cos(30.D0*deg2rad)
2889       R(1,3)=0.D0
2890       R(2,3)=0.D0
2891       R(0,4)=0.D0
2892       R(1,4)=0.D0
2893       R(2,4)=0.5D0
2894       R(0,5)=0.D0
2895       R(1,5)=cos(26.D0*deg2rad)
2896       R(2,5)=0.5D0+sin(26.D0*deg2rad)
2897       do i=1,5
2898         do j=0,2
2899           R(j,i)=vbl*R(j,i)
2900         enddo
2901       enddo
2902 !      i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2903       imov=2
2904       i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2905       print *,'RETURNED ',i
2906       print *,(R(i,3)/vbl,i=0,2)
2907
2908       return
2909       end subroutine loc_test
2910 #endif
2911 !-----------------------------------------------------------------------------
2912 ! matmult.f
2913 !-----------------------------------------------------------------------------
2914       subroutine MATMULT(A1,A2,A3)
2915 !      implicit real*8 (a-h,o-z)
2916 !      include 'DIMENSIONS'
2917 !el local variables
2918       integer :: i,j,k
2919       real(kind=8) :: A3IJ
2920
2921       real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2922       real(kind=8),DIMENSION(3,3) :: AI3
2923       DO 1 I=1,3
2924         DO 2 J=1,3
2925           A3IJ=0.0
2926           DO 3 K=1,3
2927     3       A3IJ=A3IJ+A1(I,K)*A2(K,J)
2928           AI3(I,J)=A3IJ
2929     2   CONTINUE
2930     1 CONTINUE
2931       DO 4 I=1,3
2932       DO 4 J=1,3
2933     4   A3(I,J)=AI3(I,J)
2934       return
2935       end subroutine MATMULT
2936 !-----------------------------------------------------------------------------
2937 ! readpdb.F
2938 !-----------------------------------------------------------------------------
2939       subroutine int_from_cart(lside,lprn)
2940 !      implicit real*8 (a-h,o-z)
2941 !      include 'DIMENSIONS'
2942       use control_data,only:out1file
2943 #ifdef MPI
2944       include "mpif.h"
2945 #endif
2946 !      include 'COMMON.LOCAL'
2947 !      include 'COMMON.VAR'
2948 !      include 'COMMON.CHAIN'
2949 !      include 'COMMON.INTERACT'
2950 !      include 'COMMON.IOUNITS'
2951 !      include 'COMMON.GEO'
2952 !      include 'COMMON.NAMES'
2953 !      include 'COMMON.CONTROL'
2954 !      include 'COMMON.SETUP'
2955       character(len=3) :: seq,res
2956 !      character*5 atom
2957       character(len=80) :: card
2958       real(kind=8),dimension(3,20) :: sccor
2959       integer :: i,j,iti !el  rescode,
2960       logical :: lside,lprn
2961       real(kind=8) :: di,cosfac,sinfac
2962       integer :: nres2
2963       nres2=2*nres
2964
2965       if(me.eq.king.or..not.out1file)then
2966        if (lprn) then
2967         write (iout,'(/a)') &
2968         'Internal coordinates calculated from crystal structure.'
2969         if (lside) then
2970           write (iout,'(8a)') '  Res  ','       dvb','     Theta',&
2971        '     Gamma','    Dsc_id','       Dsc','     Alpha',&
2972        '     Beta '
2973         else
2974           write (iout,'(4a)') '  Res  ','       dvb','     Theta',&
2975        '     Gamma'
2976         endif
2977        endif
2978       endif
2979       do i=1,nres-1
2980 !       if (molnum(i).ne.1) cycle
2981 !in wham      do i=1,nres
2982         iti=itype(i,1)
2983         if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2984        (iti.ne.ntyp1  .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2985           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2986 !test          stop
2987         endif
2988 !#ifndef WHAM_RUN
2989         vbld(i+1)=dist(i,i+1)
2990         vbld_inv(i+1)=1.0d0/vbld(i+1)
2991 !#endif
2992         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2993         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2994       enddo
2995 !el -----
2996 !#ifdef WHAM_RUN
2997 !      if (itype(1,1).eq.ntyp1) then
2998 !        do j=1,3
2999 !          c(j,1)=c(j,2)+(c(j,3)-c(j,4))
3000 !        enddo
3001 !      endif
3002 !      if (itype(nres,1).eq.ntyp1) then
3003 !        do j=1,3
3004 !          c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
3005 !        enddo
3006 !      endif
3007 !#endif
3008 !      if (unres_pdb) then
3009 !        if (itype(1,1).eq.21) then
3010 !          theta(3)=90.0d0*deg2rad
3011 !          phi(4)=180.0d0*deg2rad
3012 !          vbld(2)=3.8d0
3013 !          vbld_inv(2)=1.0d0/vbld(2)
3014 !        endif
3015 !        if (itype(nres,1).eq.21) then
3016 !          theta(nres)=90.0d0*deg2rad
3017 !          phi(nres)=180.0d0*deg2rad
3018 !          vbld(nres)=3.8d0
3019 !          vbld_inv(nres)=1.0d0/vbld(2)
3020 !        endif
3021 !      endif
3022       if (lside) then
3023         do i=2,nres-1
3024           do j=1,3
3025             c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
3026            +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
3027 ! in wham            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
3028           enddo
3029           iti=itype(i,1)
3030           di=dist(i,nres+i)
3031 !#ifndef WHAM_RUN
3032 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3033
3034           if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3035            di=dsc(itype(i,molnum(i)))
3036           vbld(i+nres)=di
3037           if (itype(i,1).ne.10) then
3038             vbld_inv(i+nres)=1.0d0/di
3039           else
3040             vbld_inv(i+nres)=0.0d0
3041           endif
3042 !#endif
3043           if (iti.ne.10) then
3044             alph(i)=alpha(nres+i,i,nres2+2)
3045             omeg(i)=beta(nres+i,i,nres2+2,i+1)
3046           endif
3047           if (iti.ne.0) then
3048           if(me.eq.king.or..not.out1file)then
3049            if (lprn) &
3050            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3051            rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3052            rad2deg*alph(i),rad2deg*omeg(i)
3053           endif
3054           else
3055           if(me.eq.king.or..not.out1file)then
3056            if (lprn) &
3057            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3058            rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3059            rad2deg*alph(i),rad2deg*omeg(i)
3060           endif
3061           endif
3062         enddo
3063       else if (lprn) then
3064         do i=2,nres
3065           iti=itype(i,1)
3066           if(me.eq.king.or..not.out1file) &
3067            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3068            rad2deg*theta(i),rad2deg*phi(i)
3069         enddo
3070       endif
3071       return
3072       end subroutine int_from_cart
3073 !-----------------------------------------------------------------------------
3074       subroutine sc_loc_geom(lprn)
3075 !      implicit real*8 (a-h,o-z)
3076 !      include 'DIMENSIONS'
3077       use control_data,only:out1file
3078 #ifdef MPI
3079       include "mpif.h"
3080 #endif
3081 !      include 'COMMON.LOCAL'
3082 !      include 'COMMON.VAR'
3083 !      include 'COMMON.CHAIN'
3084 !      include 'COMMON.INTERACT'
3085 !      include 'COMMON.IOUNITS'
3086 !      include 'COMMON.GEO'
3087 !      include 'COMMON.NAMES'
3088 !      include 'COMMON.CONTROL'
3089 !      include 'COMMON.SETUP'
3090       real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3091       logical :: lprn
3092 !el local variables
3093       integer :: i,j,it,iti
3094       real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3095       do i=1,nres-1
3096         do j=1,3
3097           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3098         enddo
3099       enddo
3100       do i=2,nres-1
3101         if (itype(i,1).ne.10) then
3102           do j=1,3
3103             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3104           enddo
3105         else
3106           do j=1,3
3107             dc_norm(j,i+nres)=0.0d0
3108           enddo
3109         endif
3110       enddo
3111       do i=2,nres-1
3112         costtab(i+1) =dcos(theta(i+1))
3113         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3114         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3115         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3116         cosfac2=0.5d0/(1.0d0+costtab(i+1))
3117         cosfac=dsqrt(cosfac2)
3118         sinfac2=0.5d0/(1.0d0-costtab(i+1))
3119         sinfac=dsqrt(sinfac2)
3120         it=itype(i,1)
3121
3122         if ((it.ne.10).and.(it.ne.ntyp1)) then
3123 !el        if (it.ne.10) then
3124 !
3125 !  Compute the axes of tghe local cartesian coordinates system; store in
3126 !   x_prime, y_prime and z_prime
3127 !
3128         do j=1,3
3129           x_prime(j) = 0.00
3130           y_prime(j) = 0.00
3131           z_prime(j) = 0.00
3132         enddo
3133         do j = 1,3
3134           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3135           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3136         enddo
3137         call vecpr(x_prime,y_prime,z_prime)
3138 !
3139 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3140 ! to local coordinate system. Store in xx, yy, zz.
3141 !
3142         xx=0.0d0
3143         yy=0.0d0
3144         zz=0.0d0
3145         do j = 1,3
3146           xx = xx + x_prime(j)*dc_norm(j,i+nres)
3147           yy = yy + y_prime(j)*dc_norm(j,i+nres)
3148           zz = zz + z_prime(j)*dc_norm(j,i+nres)
3149         enddo
3150
3151         xxref(i)=xx
3152         yyref(i)=yy
3153         zzref(i)=zz
3154         else
3155         xxref(i)=0.0d0
3156         yyref(i)=0.0d0
3157         zzref(i)=0.0d0
3158         endif
3159       enddo
3160       if (lprn) then
3161         do i=2,nres
3162           iti=itype(i,1)
3163           if(me.eq.king.or..not.out1file) &
3164            write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3165             yyref(i),zzref(i)
3166         enddo
3167       endif
3168
3169       return
3170       end subroutine sc_loc_geom
3171 !-----------------------------------------------------------------------------
3172       subroutine sccenter(ires,nscat,sccor)
3173 !      implicit real*8 (a-h,o-z)
3174 !      include 'DIMENSIONS'
3175 !      include 'COMMON.CHAIN'
3176       integer :: i,j,ires,nscat
3177       real(kind=8),dimension(3,20) :: sccor
3178       real(kind=8) :: sccmj
3179 !        print *,"I am in sccenter",ires,nscat
3180       do j=1,3
3181         sccmj=0.0D0
3182         do i=1,nscat
3183           sccmj=sccmj+sccor(j,i)
3184 !C          print *,"insccent", ires,sccor(j,i)
3185         enddo
3186         dc(j,ires)=sccmj/nscat
3187       enddo
3188       return
3189       end subroutine sccenter
3190 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3191 !-----------------------------------------------------------------------------
3192       subroutine bond_regular
3193       use calc_data
3194 !      implicit real*8 (a-h,o-z)
3195 !      include 'DIMENSIONS'
3196 !      include 'COMMON.VAR'
3197 !      include 'COMMON.LOCAL'
3198 !      include 'COMMON.CALC'
3199 !      include 'COMMON.INTERACT'
3200 !      include 'COMMON.CHAIN'
3201       do i=1,nres-1
3202
3203        vbld(i+1)=vbl
3204        vbld_inv(i+1)=1.0d0/vbld(i+1)
3205        vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3206        vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3207 !       print *,vbld(i+1),vbld(i+1+nres)
3208       enddo
3209       return
3210       end subroutine bond_regular
3211 #endif
3212 !-----------------------------------------------------------------------------
3213 ! refsys.f
3214 !-----------------------------------------------------------------------------
3215       subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3216 ! This subroutine calculates unit vectors of a local reference system
3217 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3218 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3219 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3220 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3221 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3222 ! form a linear fragment. Returns vectors e1, e2, and e3.
3223 !      implicit real*8 (a-h,o-z)
3224 !      include 'DIMENSIONS'
3225       logical :: fail
3226       real(kind=8),dimension(3) :: e1,e2,e3
3227       real(kind=8),dimension(3) :: u,z
3228 !      include 'COMMON.IOUNITS'
3229 !      include 'COMMON.CHAIN'
3230       real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3231 !el local variables
3232       integer :: i,i1,i2,i3,i4
3233       real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3234       fail=.false.
3235       s1=0.0
3236       s2=0.0
3237       do 1 i=1,3
3238       zi=c(i,i2)-c(i,i3)
3239       ui=c(i,i4)-c(i,i3)
3240       s1=s1+zi*zi
3241       s2=s2+ui*ui
3242       z(i)=zi
3243     1 u(i)=ui
3244       s1=sqrt(s1)
3245       s2=sqrt(s2)
3246       if (s1.gt.coinc) goto 2
3247       write (iout,1000) i2,i3,i1
3248       fail=.true.
3249 !     do 3 i=1,3
3250 !   3 c(i,i1)=0.0D0
3251       return
3252     2 if (s2.gt.coinc) goto 4
3253       write(iout,1000) i3,i4,i1
3254       fail=.true.
3255       do 5 i=1,3
3256     5 c(i,i1)=0.0D0
3257       return
3258     4 s1=1.0/s1
3259       s2=1.0/s2
3260       v1=z(2)*u(3)-z(3)*u(2)
3261       v2=z(3)*u(1)-z(1)*u(3)
3262       v3=z(1)*u(2)-z(2)*u(1)
3263       anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3264       if (anorm.gt.align) goto 6
3265       write (iout,1010) i2,i3,i4,i1
3266       fail=.true.
3267 !     do 7 i=1,3
3268 !   7 c(i,i1)=0.0D0
3269       return
3270     6 anorm=1.0D0/anorm
3271       e3(1)=v1*anorm
3272       e3(2)=v2*anorm
3273       e3(3)=v3*anorm
3274       e1(1)=z(1)*s1
3275       e1(2)=z(2)*s1
3276       e1(3)=z(3)*s1
3277       e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3278       e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3279       e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3280  1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3281        'coordinates of atom',i4,' are set to zero.')
3282  1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3283        ' fragment. coordinates of atom',i4,' are set to zero.')
3284       return
3285       end subroutine refsys
3286 !-----------------------------------------------------------------------------
3287 ! int_to_cart.f
3288 !-----------------------------------------------------------------------------
3289       subroutine int_to_cart
3290 !--------------------------------------------------------------
3291 !  This subroutine converts the energy derivatives from internal
3292 !  coordinates to cartesian coordinates
3293 !-------------------------------------------------------------
3294 !      implicit real*8 (a-h,o-z)
3295 !      include 'DIMENSIONS'
3296 !      include 'COMMON.VAR'
3297 !      include 'COMMON.CHAIN'
3298 !      include 'COMMON.DERIV'
3299 !      include 'COMMON.GEO'
3300 !      include 'COMMON.LOCAL'
3301 !      include 'COMMON.INTERACT'
3302 !      include 'COMMON.MD'
3303 !      include 'COMMON.IOUNITS'
3304 !      include 'COMMON.SCCOR'
3305 !   calculating dE/ddc1
3306 !el local variables
3307        integer :: j,i
3308 !       print *,"gloc",gloc(:,:)
3309 !       print *, "gcart",gcart(:,:)
3310        if (nres.lt.3) go to 18
3311        do j=1,3
3312          gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3313            +gloc(nres-2,icg)*dtheta(j,1,3)
3314           if ((itype(2,1).ne.10).and.&
3315           (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3316           gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3317           gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3318         endif
3319        enddo
3320 !     Calculating the remainder of dE/ddc2
3321        do j=1,3
3322          gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3323          gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3324         if(itype(2,1).ne.10) then
3325           gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3326           gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3327         endif
3328         if(itype(3,1).ne.10) then
3329           gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3330           gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3331         endif
3332         if(nres.gt.4) then
3333           gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3334         endif
3335        enddo
3336 !  If there are only five residues
3337        if(nres.eq.5) then
3338          do j=1,3
3339            gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3340            dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3341            dtheta(j,1,5)
3342 !         if(itype(3,1).ne.10) then
3343           if ((itype(3,1).ne.10).and.&
3344           (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3345            gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3346            dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3347          endif
3348 !        if(itype(4,1).ne.10) then
3349           if ((itype(4,1).ne.10).and.&
3350           (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3351            gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3352            dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3353          endif
3354         enddo
3355        endif
3356 !    If there are more than five residues
3357       if(nres.gt.5) then
3358         do i=3,nres-3
3359          do j=1,3
3360           gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3361           +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3362           gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3363           gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3364           if(itype(i,1).ne.10) then
3365            gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3366            gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3367           endif
3368           if(itype(i+1,1).ne.10) then
3369            gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3370            +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3371           endif
3372          enddo
3373         enddo
3374       endif
3375 !  Setting dE/ddnres-2
3376       if(nres.gt.5) then
3377          do j=1,3
3378            gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3379            dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3380            +gloc(2*nres-6,icg)* &
3381            dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3382           if(itype(nres-2,1).ne.10) then
3383               gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3384               dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3385               domega(j,2,nres-2)
3386           endif
3387           if(itype(nres-1,1).ne.10) then
3388              gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3389              dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3390              domega(j,1,nres-1)
3391           endif
3392          enddo
3393       endif
3394 !  Settind dE/ddnres-1
3395 !#define DEBUG
3396 #ifdef DEBUG
3397           j=1
3398               write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3399         gloc(2*nres-5,icg),dtheta(j,2,nres)
3400
3401 #endif
3402 !#undef DEBUG
3403
3404        do j=1,3
3405         gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3406         gloc(2*nres-5,icg)*dtheta(j,2,nres)
3407 !#define DEBUG
3408 #ifdef DEBUG
3409               write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3410         gloc(2*nres-5,icg),dtheta(j,2,nres)
3411
3412 #endif
3413 !#undef DEBUG
3414         if(itype(nres-1,1).ne.10) then
3415           gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3416           dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3417           domega(j,2,nres-1)
3418 !#define DEBUG
3419 #ifdef DEBUG
3420               write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3421           dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3422           domega(j,2,nres-1)
3423
3424 #endif
3425 !#undef DEBUG
3426
3427         endif
3428         enddo
3429 !   The side-chain vector derivatives
3430         do i=2,nres-1
3431          if(itype(i,1).ne.10 .and.  &
3432            itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3433             do j=1,3
3434               gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3435               +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3436 !#define DEBUG
3437 #ifdef DEBUG
3438               write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3439               gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3440 #endif
3441 !#undef DEBUG
3442             enddo
3443          endif
3444        enddo
3445 !----------------------------------------------------------------------
3446 ! INTERTYP=1 SC...Ca...Ca...Ca
3447 ! INTERTYP=2 Ca...Ca...Ca...SC
3448 ! INTERTYP=3 SC...Ca...Ca...SC
3449 !   calculating dE/ddc1
3450   18   continue
3451 !       do i=1,nres
3452 !       gloc(i,icg)=0.0D0
3453 !          write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3454 !       enddo
3455        if (nres.lt.2) return
3456        if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3457        if ((itype(1,1).ne.10).and. &
3458         (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3459         do j=1,3
3460 !c Derviative was calculated for oposite vector of side chain therefore
3461 ! there is "-" sign before gloc_sc
3462          gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3463            dtauangle(j,1,1,3)
3464          gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3465            dtauangle(j,1,2,3)
3466           if ((itype(2,1).ne.10).and. &
3467         (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3468          gxcart(j,1)= gxcart(j,1) &
3469                      -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3470          gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3471             dtauangle(j,3,2,3)
3472           endif
3473        enddo
3474        endif
3475          if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3476          (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3477       then
3478          do j=1,3
3479          gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3480          enddo
3481          endif
3482 !   As potetnial DO NOT depend on omicron anlge their derivative is
3483 !   ommited
3484 !     &     +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3485
3486 !     Calculating the remainder of dE/ddc2
3487        do j=1,3
3488          if((itype(2,1).ne.10).and. &
3489            (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3490            if ((itype(1,1).ne.10).and.&
3491               ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3492             gxcart(j,2)=gxcart(j,2)+ &
3493                                gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3494         if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3495          then
3496            gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3497 !c                  the   - above is due to different vector direction
3498            gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3499           endif
3500           if (nres.gt.3) then
3501 !           if ((itype(1,1).ne.10).and.&
3502 !              ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3503            gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3504 !c                  the   - above is due to different vector direction
3505            gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3506 !          write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3507 !           write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3508           endif
3509          endif
3510          if ((itype(1,1).ne.10).and.&
3511          (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3512           gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3513 !           write(iout,*)  gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3514         endif
3515          if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3516           gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3517 !           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3518          endif
3519          if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3520           gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3521 !           write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3522          endif
3523
3524 !      write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3525        enddo
3526 !    If there are more than five residues
3527       if(nres.ge.5) then
3528         do i=3,nres-2
3529          do j=1,3
3530 !          write(iout,*) "before", gcart(j,i)
3531           if ((itype(i,1).ne.10).and.&
3532           (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3533           gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3534           *dtauangle(j,2,3,i+1) &
3535           -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3536           gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3537           *dtauangle(j,1,2,i+2)
3538 !                   write(iout,*) "new",j,i,
3539 !     &  gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3540 !          if (itype(i-1,1).ne.10) then
3541           if ((itype(i-1,1).ne.10).and.&
3542           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3543
3544            gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3545       *dtauangle(j,3,3,i+1)
3546           endif
3547 !          if (itype(i+1,1).ne.10) then
3548           if ((itype(i+1,1).ne.10).and.&
3549           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3550           gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3551       *dtauangle(j,3,1,i+2)
3552            gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3553       *dtauangle(j,3,2,i+2)
3554           endif
3555           endif
3556 !          if (itype(i-1,1).ne.10) then
3557           if ((itype(i-1,1).ne.10).and.&
3558           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3559            gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3560            dtauangle(j,1,3,i+1)
3561           endif
3562 !          if (itype(i+1,1).ne.10) then
3563           if ((itype(i+1,1).ne.10).and.&
3564           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3565            gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3566            dtauangle(j,2,2,i+2)
3567 !          write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3568 !     &    dtauangle(j,2,2,i+2)
3569           endif
3570 !          if (itype(i+2,1).ne.10) then
3571           if ((itype(i+2,1).ne.10).and.&
3572           (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3573            gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3574            dtauangle(j,2,1,i+3)
3575           endif
3576          enddo
3577         enddo
3578       endif
3579 !  Setting dE/ddnres-1
3580       if(nres.ge.4) then
3581          do j=1,3
3582          if ((itype(nres-1,1).ne.10).and.&
3583        (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3584          gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3585           *dtauangle(j,2,3,nres)
3586 !          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3587 !     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
3588 !         if (itype(nres-2,1).ne.10) then
3589          if ((itype(nres-2,1).ne.10).and.&
3590        (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3591        gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3592           *dtauangle(j,3,3,nres)
3593           endif
3594          if ((itype(nres,1).ne.10).and.&
3595          (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3596         gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3597           *dtauangle(j,3,1,nres+1)
3598         gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3599           *dtauangle(j,3,2,nres+1)
3600           endif
3601          endif
3602          if ((itype(nres-2,1).ne.10).and.&
3603          (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3604             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3605          dtauangle(j,1,3,nres)
3606          endif
3607           if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3608             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3609            dtauangle(j,2,2,nres+1)
3610 !           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3611 !     &     dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3612            endif
3613          enddo
3614       endif
3615 !  Settind dE/ddnres
3616        if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3617           (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3618        do j=1,3
3619         gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3620        *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3621        *dtauangle(j,2,3,nres+1)
3622         enddo
3623        endif
3624 !   The side-chain vector derivatives
3625 !       print *,"gcart",gcart(:,:)
3626       return
3627       end subroutine int_to_cart
3628 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3629 !-----------------------------------------------------------------------------
3630 ! readrtns_CSA.F
3631 !-----------------------------------------------------------------------------
3632       subroutine gen_dist_constr
3633 ! Generate CA distance constraints.
3634 !      implicit real*8 (a-h,o-z)
3635 !      include 'DIMENSIONS'
3636 !      include 'COMMON.IOUNITS'
3637 !      include 'COMMON.GEO'
3638 !      include 'COMMON.VAR'
3639 !      include 'COMMON.INTERACT'
3640 !      include 'COMMON.LOCAL'
3641 !      include 'COMMON.NAMES'
3642 !      include 'COMMON.CHAIN'
3643 !      include 'COMMON.FFIELD'
3644 !      include 'COMMON.SBRIDGE'
3645 !      include 'COMMON.HEADER'
3646 !      include 'COMMON.CONTROL'
3647 !      include 'COMMON.DBASE'
3648 !      include 'COMMON.THREAD'
3649 !      include 'COMMON.TIME1'
3650 !      integer :: itype_pdb !(maxres)
3651 !      common /pizda/ itype_pdb(nres)
3652       character(len=2) :: iden
3653 !el local variables
3654       integer :: i,j
3655 !d      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3656 !d      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3657 !d     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3658 !d     & ' nsup',nsup
3659       do i=nstart_sup,nstart_sup+nsup-1
3660 !d      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3661 !d     &    ' seq_pdb', restyp(itype_pdb(i))
3662         do j=i+2,nstart_sup+nsup-1
3663           nhpb=nhpb+1
3664           ihpb(nhpb)=i+nstart_seq-nstart_sup
3665           jhpb(nhpb)=j+nstart_seq-nstart_sup
3666           forcon(nhpb)=weidis
3667           dhpb(nhpb)=dist(i,j)
3668         enddo
3669       enddo
3670 !d      write (iout,'(a)') 'Distance constraints:'
3671 !d      do i=nss+1,nhpb
3672 !d        ii=ihpb(i)
3673 !d        jj=jhpb(i)
3674 !d        iden='CA'
3675 !d        if (ii.gt.nres) then
3676 !d          iden='SC'
3677 !d          ii=ii-nres
3678 !d          jj=jj-nres
3679 !d        endif
3680 !d        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3681 !d     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3682 !d     &  dhpb(i),forcon(i)
3683 !d      enddo
3684 !      deallocate(itype_pdb)
3685
3686       return
3687       end subroutine gen_dist_constr
3688 #endif
3689 !-----------------------------------------------------------------------------
3690 ! cartprint.f
3691 !-----------------------------------------------------------------------------
3692       subroutine cartprint
3693
3694       use geometry_data, only: c
3695       use energy_data, only: itype
3696 !      implicit real*8 (a-h,o-z)
3697 !      include 'DIMENSIONS'
3698 !      include 'COMMON.CHAIN'
3699 !      include 'COMMON.INTERACT'
3700 !      include 'COMMON.NAMES'
3701 !      include 'COMMON.IOUNITS'
3702       integer :: i
3703
3704       write (iout,100)
3705       do i=1,nres
3706         write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3707           c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3708       enddo
3709   100 format (//'              alpha-carbon coordinates       ',&
3710                 '     centroid coordinates'/ &
3711                 '       ', 6X,'X',11X,'Y',11X,'Z',&
3712                                 10X,'X',11X,'Y',11X,'Z')
3713   110 format (a,'(',i3,')',6f12.5)
3714       return
3715       end subroutine cartprint
3716 !-----------------------------------------------------------------------------
3717 !-----------------------------------------------------------------------------
3718       subroutine alloc_geo_arrays
3719 !EL Allocation of tables used by module energy
3720
3721       integer :: i,j,nres2
3722       nres2=2*nres
3723 ! commom.bounds
3724 !      common /bounds/
3725       allocate(phibound(2,nres+2)) !(2,maxres)
3726 !----------------------
3727 ! commom.chain
3728 !      common /chain/ in molread
3729 !      real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3730 !      real(kind=8),dimension(:,:),allocatable :: dc
3731       allocate(dc_old(3,0:nres2))
3732 !      if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3733       if(.not.allocated(dc_norm2)) then
3734         allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3735         dc_norm2(:,:)=0.d0
3736       endif
3737 !
3738 !el      if(.not.allocated(dc_norm))
3739 !elwrite(iout,*) "jestem w alloc geo 1"
3740       if(.not.allocated(dc_norm)) then
3741         allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3742         dc_norm(:,:)=0.d0
3743       endif
3744 !elwrite(iout,*) "jestem w alloc geo 1"
3745       allocate(xloc(3,nres),xrot(3,nres))
3746 !elwrite(iout,*) "jestem w alloc geo 1"
3747       xloc(:,:)=0.0D0
3748 !elwrite(iout,*) "jestem w alloc geo 1"
3749       allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3750 !      common /rotmat/
3751       allocate(t(3,3,nres),r(3,3,nres))
3752       allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3753 !      common /refstruct/
3754       if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3755 !elwrite(iout,*) "jestem w alloc geo 2"
3756       allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3757       if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3758       if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3759 !      common /from_zscore/ in module.compare
3760 !----------------------
3761 ! common.local
3762 ! Inverses of the actual virtual bond lengths
3763 !      common /invlen/ in io_conf: molread or readpdb
3764 !      real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3765 !----------------------
3766 ! common.var
3767 ! Store the geometric variables in the following COMMON block.
3768 !      common /var/ in readpdb or ...
3769       if(.not.allocated(theta)) allocate(theta(nres+2))
3770       if(.not.allocated(phi)) allocate(phi(nres+2))
3771       if(.not.allocated(alph)) allocate(alph(nres+2))
3772       if(.not.allocated(omeg)) allocate(omeg(nres+2))
3773       if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3774       if(.not.allocated(phiref)) allocate(phiref(nres+2))
3775       if(.not.allocated(costtab)) allocate(costtab(nres))
3776       if(.not.allocated(sinttab)) allocate(sinttab(nres))
3777       if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3778       if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3779 !      real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3780       allocate(omicron(2,nres+2)) !(2,maxres)
3781       allocate(tauangle(3,nres+2)) !(3,maxres)
3782 !elwrite(iout,*) "jestem w alloc geo 3"
3783       if(.not.allocated(xxtab)) allocate(xxtab(nres))
3784       if(.not.allocated(yytab)) allocate(yytab(nres))
3785       if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3786       if(.not.allocated(xxref)) allocate(xxref(nres))
3787       if(.not.allocated(yyref)) allocate(yyref(nres))
3788       if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3789       allocate(ialph(nres,2)) !(maxres,2)
3790       ialph(:,1)=0
3791       ialph(:,2)=0
3792       allocate(ivar(4*nres2)) !(4*maxres2)
3793
3794 #if defined(WHAM_RUN) || defined(CLUSTER)
3795       allocate(vbld(2*nres))
3796       vbld(:)=0.d0
3797       allocate(vbld_inv(2*nres))
3798       vbld_inv(:)=0.d0
3799 #endif
3800
3801       return
3802       end subroutine alloc_geo_arrays
3803 !-----------------------------------------------------------------------------
3804 !-----------------------------------------------------------------------------
3805       subroutine returnbox
3806       integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3807       integer :: chain_end,ireturnval
3808       real*8 :: difference
3809 !C change suggested by Ana - end
3810         j=1
3811         chain_beg=1
3812 !C        do i=1,nres
3813 !C       write(*,*) 'initial', i,j,c(j,i)
3814 !C        enddo
3815 !C change suggested by Ana - begin
3816         allareout=1
3817 !C change suggested by Ana -end
3818         do i=1,nres-1
3819            mnum=molnum(i)
3820          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3821             .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3822           chain_end=i
3823           if (allareout.eq.1) then
3824             ireturnval=int(c(j,i)/boxxsize)
3825             if (c(j,i).le.0) ireturnval=ireturnval-1
3826             do k=chain_beg,chain_end
3827               c(j,k)=c(j,k)-ireturnval*boxxsize
3828               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3829             enddo
3830 !C Suggested by Ana
3831             if (chain_beg.eq.1) &
3832             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3833 !C Suggested by Ana -end
3834            endif
3835            chain_beg=i+1
3836            allareout=1
3837          else
3838           if (int(c(j,i)/boxxsize).eq.0) allareout=0
3839          endif
3840         enddo
3841          if (allareout.eq.1) then
3842             ireturnval=int(c(j,i)/boxxsize)
3843             if (c(j,i).le.0) ireturnval=ireturnval-1
3844             do k=chain_beg,nres
3845               c(j,k)=c(j,k)-ireturnval*boxxsize
3846               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3847             enddo
3848           endif
3849 !C NO JUMP
3850 !C        do i=1,nres
3851 !C        write(*,*) 'befor no jump', i,j,c(j,i)
3852 !C        enddo
3853         nojumpval=0
3854         do i=2,nres
3855            mnum=molnum(i)
3856            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3857               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3858              difference=abs(c(j,i-1)-c(j,i))
3859 !C             print *,'diff', difference
3860              if (difference.gt.boxxsize/2.0) then
3861                 if (c(j,i-1).gt.c(j,i)) then
3862                   nojumpval=1
3863                  else
3864                    nojumpval=-1
3865                  endif
3866               else
3867               nojumpval=0
3868               endif
3869               endif
3870               c(j,i)=c(j,i)+nojumpval*boxxsize
3871               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3872          enddo
3873        nojumpval=0
3874         do i=2,nres
3875            mnum=molnum(i)
3876            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3877              difference=abs(c(j,i-1)-c(j,i))
3878              if (difference.gt.boxxsize/2.0) then
3879                 if (c(j,i-1).gt.c(j,i)) then
3880                   nojumpval=1
3881                  else
3882                    nojumpval=-1
3883                  endif
3884               else
3885               nojumpval=0
3886               endif
3887              endif
3888               c(j,i)=c(j,i)+nojumpval*boxxsize
3889               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3890          enddo
3891
3892 !C        do i=1,nres
3893 !C        write(*,*) 'after no jump', i,j,c(j,i)
3894 !C        enddo
3895
3896 !C NOW Y dimension
3897 !C suggesed by Ana begins
3898         allareout=1
3899         j=2
3900         chain_beg=1
3901         do i=1,nres-1
3902            mnum=molnum(i)
3903          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3904            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3905           chain_end=i
3906           if (allareout.eq.1) then
3907             ireturnval=int(c(j,i)/boxysize)
3908             if (c(j,i).le.0) ireturnval=ireturnval-1
3909             do k=chain_beg,chain_end
3910               c(j,k)=c(j,k)-ireturnval*boxysize
3911              c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3912             enddo
3913 !C Suggested by Ana
3914             if (chain_beg.eq.1) &
3915             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3916 !C Suggested by Ana -end
3917            endif
3918            chain_beg=i+1
3919            allareout=1
3920          else
3921           if (int(c(j,i)/boxysize).eq.0) allareout=0
3922          endif
3923         enddo
3924          if (allareout.eq.1) then
3925             ireturnval=int(c(j,i)/boxysize)
3926             if (c(j,i).le.0) ireturnval=ireturnval-1
3927             do k=chain_beg,nres
3928               c(j,k)=c(j,k)-ireturnval*boxysize
3929               c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3930             enddo
3931           endif
3932         nojumpval=0
3933         do i=2,nres
3934            mnum=molnum(i)
3935            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3936               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3937              difference=abs(c(j,i-1)-c(j,i))
3938              if (difference.gt.boxysize/2.0) then
3939                 if (c(j,i-1).gt.c(j,i)) then
3940                   nojumpval=1
3941                  else
3942                    nojumpval=-1
3943                  endif
3944              else
3945               nojumpval=0
3946               endif
3947            endif
3948               c(j,i)=c(j,i)+nojumpval*boxysize
3949               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3950          enddo
3951       nojumpval=0
3952         do i=2,nres
3953            mnum=molnum(i)
3954            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3955              .and. itype(i-1,mnum).eq.ntyp1) then
3956              difference=abs(c(j,i-1)-c(j,i))
3957              if (difference.gt.boxysize/2.0) then
3958                 if (c(j,i-1).gt.c(j,i)) then
3959                   nojumpval=1
3960                  else
3961                    nojumpval=-1
3962                  endif
3963               else
3964               nojumpval=0
3965               endif
3966             endif
3967               c(j,i)=c(j,i)+nojumpval*boxysize
3968               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3969          enddo
3970 !C Now Z dimension
3971 !C Suggested by Ana -begins
3972         allareout=1
3973 !C Suggested by Ana -ends
3974        j=3
3975         chain_beg=1
3976         do i=1,nres-1
3977            mnum=molnum(i)
3978          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3979            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3980           chain_end=i
3981           if (allareout.eq.1) then
3982             ireturnval=int(c(j,i)/boxysize)
3983             if (c(j,i).le.0) ireturnval=ireturnval-1
3984             do k=chain_beg,chain_end
3985               c(j,k)=c(j,k)-ireturnval*boxzsize
3986               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3987             enddo
3988 !C Suggested by Ana
3989             if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3990 !C Suggested by Ana -end
3991            endif
3992            chain_beg=i+1
3993            allareout=1
3994          else
3995           if (int(c(j,i)/boxzsize).eq.0) allareout=0
3996          endif
3997         enddo
3998          if (allareout.eq.1) then
3999             ireturnval=int(c(j,i)/boxzsize)
4000             if (c(j,i).le.0) ireturnval=ireturnval-1
4001             do k=chain_beg,nres
4002               c(j,k)=c(j,k)-ireturnval*boxzsize
4003               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
4004             enddo
4005           endif
4006         nojumpval=0
4007         do i=2,nres
4008            mnum=molnum(i)
4009            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4010              difference=abs(c(j,i-1)-c(j,i))
4011              if (difference.gt.(boxzsize/2.0)) then
4012                 if (c(j,i-1).gt.c(j,i)) then
4013                   nojumpval=1
4014                  else
4015                    nojumpval=-1
4016                  endif
4017               else
4018               nojumpval=0
4019               endif
4020             endif
4021               c(j,i)=c(j,i)+nojumpval*boxzsize
4022               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4023          enddo
4024        nojumpval=0
4025         do i=2,nres
4026            mnum=molnum(i)
4027            if (itype(i,mnum).eq.ntyp1_molec(mnum) &
4028             .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4029              difference=abs(c(j,i-1)-c(j,i))
4030              if (difference.gt.boxzsize/2.0) then
4031                 if (c(j,i-1).gt.c(j,i)) then
4032                   nojumpval=1
4033                  else
4034                    nojumpval=-1
4035                  endif
4036               else
4037               nojumpval=0
4038               endif
4039             endif
4040              c(j,i)=c(j,i)+nojumpval*boxzsize
4041               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4042          enddo
4043         do i=1,nres
4044          if (molnum(i).eq.5) then
4045           c(1,i)=dmod(c(1,i),boxxsize)
4046           c(2,i)=dmod(c(2,i),boxysize)
4047           c(3,i)=dmod(c(3,i),boxzsize)
4048           c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4049           c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4050           c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4051          endif
4052         enddo
4053         return
4054         end       subroutine returnbox
4055 !-------------------------------------------------------------------------------------------------------
4056       end module geometry