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/2)
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 !      print *,"TUT?",om1*chiom1,facsig,om1,om2,om12
1646       sigsq=1.0D0-facsig*faceps1_inv
1647       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1648       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1649       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1650 ! diagnostics only
1651 !      sigsq=1.0d0
1652 !      sigsq_om1=0.0d0
1653 !      sigsq_om2=0.0d0
1654 !      sigsq_om12=0.0d0
1655 !      write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1656 !      write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1657 !     &    " eps1",eps1
1658 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1659       chipom1=chip1*om1
1660       chipom2=chip2*om2
1661       chipom12=chip12*om12
1662       facp=1.0D0-om12*chipom12
1663       facp_inv=1.0D0/facp
1664       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1665 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1666 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1667 ! Following variable is the square root of eps2
1668       eps2rt=1.0D0-facp1*facp_inv
1669 ! Following three variables are the derivatives of the square root of eps
1670 ! in om1, om2, and om12.
1671       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1672       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1673       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1674 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1675       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1676 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1677 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1678 !     &  " eps2rt_om12",eps2rt_om12
1679 ! Calculate whole angle-dependent part of epsilon and contributions
1680 ! to its derivatives
1681       return
1682       end subroutine sc_angular
1683 !-----------------------------------------------------------------------------
1684 ! initialize_p.F
1685       subroutine sc_angular_nucl
1686 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1687 ! om12. Called by ebp, egb, and egbv.
1688 !      use calc_data
1689 !      implicit none
1690 !      include 'COMMON.CALC'
1691 !      include 'COMMON.IOUNITS'
1692       use comm_locel
1693       use calc_data_nucl
1694       erij(1)=xj*rij
1695       erij(2)=yj*rij
1696       erij(3)=zj*rij
1697       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1698       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1699       om12=dxi*dxj+dyi*dyj+dzi*dzj
1700       chiom12=chi12*om12
1701 ! Calculate eps1(om12) and its derivative in om12
1702       faceps1=1.0D0-om12*chiom12
1703       faceps1_inv=1.0D0/faceps1
1704       eps1=dsqrt(faceps1_inv)
1705 ! Following variable is eps1*deps1/dom12
1706       eps1_om12=faceps1_inv*chiom12
1707 ! diagnostics only
1708 !      faceps1_inv=om12
1709 !      eps1=om12
1710 !      eps1_om12=1.0d0
1711 !      write (iout,*) "om12",om12," eps1",eps1
1712 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1713 ! and om12.
1714       om1om2=om1*om2
1715       chiom1=chi1*om1
1716       chiom2=chi2*om2
1717       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1718       sigsq=1.0D0-facsig*faceps1_inv
1719       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1720       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1721       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1722       chipom1=chip1*om1
1723       chipom2=chip2*om2
1724       chipom12=chip12*om12
1725       facp=1.0D0-om12*chipom12
1726       facp_inv=1.0D0/facp
1727       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1728 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1729 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1730 ! Following variable is the square root of eps2
1731       eps2rt=1.0D0-facp1*facp_inv
1732 ! Following three variables are the derivatives of the square root of eps
1733 ! in om1, om2, and om12.
1734       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1735       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1736       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1737 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1738       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1739 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1740 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1741 !     &  " eps2rt_om12",eps2rt_om12
1742 ! Calculate whole angle-dependent part of epsilon and contributions
1743 ! to its derivatives
1744       return
1745       end subroutine sc_angular_nucl
1746
1747 !-----------------------------------------------------------------------------
1748       subroutine int_bounds(total_ints,lower_bound,upper_bound)
1749 !      implicit real*8 (a-h,o-z)
1750 !      include 'DIMENSIONS'
1751       include 'mpif.h'
1752 !      include 'COMMON.SETUP'
1753       integer :: total_ints,lower_bound,upper_bound,nint
1754       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1755       integer :: i,nexcess
1756       nint=total_ints/nfgtasks
1757       do i=1,nfgtasks
1758         int4proc(i-1)=nint
1759       enddo
1760       nexcess=total_ints-nint*nfgtasks
1761       do i=1,nexcess
1762         int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1763       enddo
1764       lower_bound=0
1765       do i=0,fg_rank-1
1766         lower_bound=lower_bound+int4proc(i)
1767       enddo
1768       upper_bound=lower_bound+int4proc(fg_rank)
1769       lower_bound=lower_bound+1
1770       return
1771       end subroutine int_bounds
1772 !-----------------------------------------------------------------------------
1773       subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1774 !      implicit real*8 (a-h,o-z)
1775 !      include 'DIMENSIONS'
1776       include 'mpif.h'
1777 !      include 'COMMON.SETUP'
1778       integer :: total_ints,lower_bound,upper_bound,nint
1779       integer :: nexcess,i
1780       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1781       nint=total_ints/nfgtasks1
1782       do i=1,nfgtasks1
1783         int4proc(i-1)=nint
1784       enddo
1785       nexcess=total_ints-nint*nfgtasks1
1786       do i=1,nexcess
1787         int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1788       enddo
1789       lower_bound=0
1790       do i=0,fg_rank1-1
1791         lower_bound=lower_bound+int4proc(i)
1792       enddo
1793       upper_bound=lower_bound+int4proc(fg_rank1)
1794       lower_bound=lower_bound+1
1795       return
1796       end subroutine int_bounds1
1797 !-----------------------------------------------------------------------------
1798 ! intcartderiv.F
1799 !-----------------------------------------------------------------------------
1800       subroutine chainbuild_cart
1801 !      implicit real*8 (a-h,o-z)
1802 !      include 'DIMENSIONS'
1803       use control_data
1804 #ifdef MPI
1805       include 'mpif.h'
1806 #endif
1807 !      include 'COMMON.SETUP'
1808 !      include 'COMMON.CHAIN'
1809 !      include 'COMMON.LOCAL'
1810 !      include 'COMMON.TIME1'
1811 !      include 'COMMON.IOUNITS'
1812       integer :: j,i,ierror,ierr
1813       real(kind=8) :: time00,time01
1814 #ifdef MPI
1815       if (nfgtasks.gt.1) then
1816 !        write (iout,*) "BCAST in chainbuild_cart"
1817 !        call flush(iout)
1818 ! Broadcast the order to build the chain and compute internal coordinates
1819 ! to the slaves. The slaves receive the order in ERGASTULUM.
1820         time00=MPI_Wtime()
1821 !      write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1822 !      do i=0,nres
1823 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1824 !     &   (dc(j,i+nres),j=1,3)
1825 !      enddo
1826         if (fg_rank.eq.0) &
1827           call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1828         time_bcast7=time_bcast7+MPI_Wtime()-time00
1829         time01=MPI_Wtime()
1830         call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1831           king,FG_COMM,IERR)
1832 !      write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1833 !      do i=0,nres
1834 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1835 !     &   (dc(j,i+nres),j=1,3)
1836 !      enddo
1837 !        write (iout,*) "End BCAST in chainbuild_cart"
1838 !        call flush(iout)
1839         time_bcast=time_bcast+MPI_Wtime()-time00
1840         time_bcastc=time_bcastc+MPI_Wtime()-time01
1841       endif
1842 #endif
1843       do j=1,3
1844         c(j,1)=dc(j,0)
1845       enddo
1846       do i=2,nres
1847         do j=1,3
1848           c(j,i)=c(j,i-1)+dc(j,i-1)
1849         enddo
1850       enddo
1851       do i=1,nres
1852         do j=1,3
1853           c(j,i+nres)=c(j,i)+dc(j,i+nres)
1854         enddo
1855       enddo
1856 !      write (iout,*) "CHAINBUILD_CART"
1857 !      call cartprint
1858       call int_from_cart1(.false.)
1859       return
1860       end subroutine chainbuild_cart
1861 !-----------------------------------------------------------------------------
1862 ! intcor.f
1863 !-----------------------------------------------------------------------------
1864       real(kind=8) function alpha(i1,i2,i3)
1865 !
1866 !  Calculates the planar angle between atoms (i1), (i2), and (i3).
1867 !
1868 !      implicit real*8 (a-h,o-z)
1869 !      include 'DIMENSIONS'
1870 !      include 'COMMON.GEO'
1871 !      include 'COMMON.CHAIN'
1872 !el local variables
1873       integer :: i1,i2,i3
1874       real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1875       x12=c(1,i1)-c(1,i2)
1876       x23=c(1,i3)-c(1,i2)
1877       y12=c(2,i1)-c(2,i2)
1878       y23=c(2,i3)-c(2,i2)
1879       z12=c(3,i1)-c(3,i2)
1880       z23=c(3,i3)-c(3,i2)
1881       vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1882       wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1883       scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1884       alpha=arcos(scalar)
1885       return
1886       end function alpha
1887 !-----------------------------------------------------------------------------
1888       real(kind=8) function beta(i1,i2,i3,i4)
1889 !
1890 !  Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1891 !
1892 !      implicit real*8 (a-h,o-z)
1893 !      include 'DIMENSIONS'
1894 !      include 'COMMON.GEO'
1895 !      include 'COMMON.CHAIN'
1896 !el local variables
1897       integer :: i1,i2,i3,i4
1898       real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1899       real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1900       real(kind=8) :: tx,ty,tz
1901       x12=c(1,i1)-c(1,i2)
1902       x23=c(1,i3)-c(1,i2)
1903       x34=c(1,i4)-c(1,i3)
1904       y12=c(2,i1)-c(2,i2)
1905       y23=c(2,i3)-c(2,i2)
1906       y34=c(2,i4)-c(2,i3)
1907       z12=c(3,i1)-c(3,i2)
1908       z23=c(3,i3)-c(3,i2)
1909       z34=c(3,i4)-c(3,i3)
1910 !d    print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1911 !d    print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1912 !d    print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1913       wx=-y23*z34+y34*z23
1914       wy=x23*z34-z23*x34
1915       wz=-x23*y34+y23*x34
1916       wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1917       vx=y12*z23-z12*y23
1918       vy=-x12*z23+z12*x23
1919       vz=x12*y23-y12*x23
1920       vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1921       if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1922       scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1923       if (dabs(scalar).gt.1.0D0) &
1924       scalar=0.99999999999999D0*scalar/dabs(scalar)
1925       angle=dacos(scalar)
1926 !d    print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1927 !d   &scalar,angle
1928       else
1929       angle=pi
1930       endif
1931 !     if (angle.le.0.0D0) angle=pi+angle
1932       tx=vy*wz-vz*wy
1933       ty=-vx*wz+vz*wx
1934       tz=vx*wy-vy*wx
1935       scalar=tx*x23+ty*y23+tz*z23
1936       if (scalar.lt.0.0D0) angle=-angle
1937       beta=angle
1938       return
1939       end function beta
1940 !-----------------------------------------------------------------------------
1941       real(kind=8) function dist(i1,i2)
1942 !
1943 !  Calculates the distance between atoms (i1) and (i2).
1944 !
1945 !      implicit real*8 (a-h,o-z)
1946 !      include 'DIMENSIONS'
1947 !      include 'COMMON.GEO'
1948 !      include 'COMMON.CHAIN'
1949 !el local variables
1950       integer :: i1,i2
1951       real(kind=8) :: x12,y12,z12
1952       x12=c(1,i1)-c(1,i2)
1953       y12=c(2,i1)-c(2,i2)
1954       z12=c(3,i1)-c(3,i2)
1955       dist=dsqrt(x12*x12+y12*y12+z12*z12)
1956       return
1957       end function dist
1958 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1959 !-----------------------------------------------------------------------------
1960 ! local_move.f
1961 !-----------------------------------------------------------------------------
1962       subroutine local_move_init(debug)
1963 !rc      implicit none
1964
1965 !     Includes
1966 !      implicit real*8 (a-h,o-z)
1967 !      include 'DIMENSIONS'  ! Needed by COMMON.LOCAL
1968 !      include 'COMMON.GEO'  ! For pi, deg2rad
1969 !      include 'COMMON.LOCAL'  ! For vbl
1970 !      include 'COMMON.LOCMOVE'
1971
1972 !     INPUT arguments
1973       logical :: debug
1974
1975
1976 !     Determine wheter to do some debugging output
1977       locmove_output=debug
1978
1979 !     Set the init_called flag to 1
1980       init_called=1
1981
1982 !     The following are never changed
1983       min_theta=60.D0*deg2rad  ! (0,PI)
1984       max_theta=175.D0*deg2rad  ! (0,PI)
1985       dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1986       dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1987       flag=1.0D300
1988       small=1.0D-5
1989       small2=0.5*small*small
1990
1991 !     Not really necessary...
1992       a_n=0
1993       b_n=0
1994       res_n=0
1995
1996       return
1997       end subroutine local_move_init
1998 !-----------------------------------------------------------------------------
1999       subroutine local_move(n_start, n_end, PHImin, PHImax)
2000 !     Perform a local move between residues m and n (inclusive)
2001 !     PHImin and PHImax [0,PI] determine the size of the move
2002 !     Works on whatever structure is in the variables theta and phi,
2003 !     sidechain variables are left untouched
2004 !     The final structure is NOT minimized, but both the cartesian
2005 !     variables c and the angles are up-to-date at the end (no further
2006 !     chainbuild is required)
2007 !rc      implicit none
2008       use random,only:ran_number
2009 !     Includes
2010 !      implicit real*8 (a-h,o-z)
2011 !      include 'DIMENSIONS'
2012 !      include 'COMMON.GEO'
2013 !      include 'COMMON.CHAIN'
2014 !      include 'COMMON.VAR'
2015 !      include 'COMMON.MINIM'
2016 !      include 'COMMON.SBRIDGE'
2017 !      include 'COMMON.LOCMOVE'
2018
2019 !     External functions
2020 !EL      integer move_res
2021 !EL      external move_res
2022 !EL      double precision ran_number
2023 !EL      external ran_number
2024
2025 !     INPUT arguments
2026       integer :: n_start, n_end  ! First and last residues to move
2027       real(kind=8) :: PHImin, PHImax  ! min/max angles [0,PI]
2028
2029 !     Local variables
2030       integer :: i,j
2031       real(kind=8) :: min,max
2032       integer :: iretcode
2033
2034
2035 !     Check if local_move_init was called.  This assumes that it
2036 !     would not be 1 if not explicitely initialized
2037       if (init_called.ne.1) then
2038         write(6,*)'   ***   local_move_init not called!!!'
2039         stop
2040       endif
2041
2042 !     Quick check for crazy range
2043       if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2044         write(6,'(a,i3,a,i3)') &
2045              '   ***   Cannot make local move between n_start = ',&
2046              n_start,' and n_end = ',n_end
2047         return
2048       endif
2049
2050 !     Take care of end residues first...
2051       if (n_start.eq.1) then
2052 !     Move residue 1 (completely random)
2053         theta(3)=ran_number(min_theta,max_theta)
2054         phi(4)=ran_number(-PI,PI)
2055         i=2
2056       else
2057         i=n_start
2058       endif
2059       if (n_end.eq.nres) then
2060 !     Move residue nres (completely random)
2061         theta(nres)=ran_number(min_theta,max_theta)
2062         phi(nres)=ran_number(-PI,PI)
2063         j=nres-1
2064       else
2065         j=n_end
2066       endif
2067
2068 !     ...then go through all other residues one by one
2069 !     Start from the two extremes and converge
2070       call chainbuild
2071       do while (i.le.j)
2072         min=PHImin
2073         max=PHImax
2074 !$$$c     Move the first two residues by less than the others
2075 !$$$        if (i-n_start.lt.3) then
2076 !$$$          if (i-n_start.eq.0) then
2077 !$$$            min=0.4*PHImin
2078 !$$$            max=0.4*PHImax
2079 !$$$          else if (i-n_start.eq.1) then
2080 !$$$            min=0.8*PHImin
2081 !$$$            max=0.8*PHImax
2082 !$$$          else if (i-n_start.eq.2) then
2083 !$$$            min=PHImin
2084 !$$$            max=PHImax
2085 !$$$          endif
2086 !$$$        endif
2087
2088 !     The actual move, on residue i
2089         iretcode=move_res(min,max,i)  ! Discard iretcode
2090         i=i+1
2091
2092         if (i.le.j) then
2093           min=PHImin
2094           max=PHImax
2095 !$$$c     Move the last two residues by less than the others
2096 !$$$          if (n_end-j.lt.3) then
2097 !$$$            if (n_end-j.eq.0) then
2098 !$$$              min=0.4*PHImin
2099 !$$$              max=0.4*PHImax
2100 !$$$            else if (n_end-j.eq.1) then
2101 !$$$              min=0.8*PHImin
2102 !$$$              max=0.8*PHImax
2103 !$$$            else if (n_end-j.eq.2) then
2104 !$$$              min=PHImin
2105 !$$$              max=PHImax
2106 !$$$            endif
2107 !$$$          endif
2108
2109 !     The actual move, on residue j
2110           iretcode=move_res(min,max,j)  ! Discard iretcode
2111           j=j-1
2112         endif
2113       enddo
2114
2115       call int_from_cart(.false.,.false.)
2116
2117       return
2118       end subroutine local_move
2119 !-----------------------------------------------------------------------------
2120       subroutine output_tabs
2121 !     Prints out the contents of a_..., b_..., res_...
2122 !      implicit none
2123
2124 !     Includes
2125 !      include 'COMMON.GEO'
2126 !      include 'COMMON.LOCMOVE'
2127
2128 !     Local variables
2129       integer :: i,j
2130
2131       write(6,*)'a_...'
2132       write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2133       write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2134
2135       write(6,*)'b_...'
2136       write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2137       write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2138
2139       write(6,*)'res_...'
2140       write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2141       write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2142       write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2143       write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2144
2145       return
2146       end subroutine output_tabs
2147 !-----------------------------------------------------------------------------
2148       subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2149 !     Only uses angles if [0,PI] (but PHImin cannot be 0.,
2150 !     and PHImax cannot be PI)
2151 !      implicit none
2152
2153 !     Includes
2154 !      include 'COMMON.GEO'
2155
2156 !     INPUT arguments
2157       real(kind=8) :: PHImin,PHImax
2158
2159 !     OUTPUT arguments
2160       integer :: n
2161       real(kind=8),dimension(0:3) :: ang
2162       logical,dimension(0:2,0:3) :: tab
2163
2164
2165       if (PHImin .eq. PHImax) then
2166 !     Special case with two 010's
2167         n = 2;
2168         ang(0) = -PHImin;
2169         ang(1) = PHImin;
2170         tab(0,0) = .false.
2171         tab(2,0) = .false.
2172         tab(0,1) = .false.
2173         tab(2,1) = .false.
2174         tab(1,0) = .true.
2175         tab(1,1) = .true.
2176       else if (PHImin .eq. PI) then
2177 !     Special case with one 010
2178         n = 1
2179         ang(0) = PI
2180         tab(0,0) = .false.
2181         tab(2,0) = .false.
2182         tab(1,0) = .true.
2183       else if (PHImax .eq. 0.) then
2184 !     Special case with one 010
2185         n = 1
2186         ang(0) = 0.
2187         tab(0,0) = .false.
2188         tab(2,0) = .false.
2189         tab(1,0) = .true.
2190       else
2191 !     Standard cases
2192         n = 0
2193         if (PHImin .gt. 0.) then
2194 !     Start of range (011)
2195           ang(n) = PHImin
2196           tab(0,n) = .false.
2197           tab(1,n) = .true.
2198           tab(2,n) = .true.
2199 !     End of range (110)
2200           ang(n+1) = -PHImin
2201           tab(0,n+1) = .true.
2202           tab(1,n+1) = .true.
2203           tab(2,n+1) = .false.
2204           n = n+2
2205         endif
2206         if (PHImax .lt. PI) then
2207 !     Start of range (011)
2208           ang(n) = -PHImax
2209           tab(0,n) = .false.
2210           tab(1,n) = .true.
2211           tab(2,n) = .true.
2212 !     End of range (110)
2213           ang(n+1) = PHImax
2214           tab(0,n+1) = .true.
2215           tab(1,n+1) = .true.
2216           tab(2,n+1) = .false.
2217           n = n+2
2218         endif
2219       endif
2220
2221       return
2222       end subroutine angles2tab
2223 !-----------------------------------------------------------------------------
2224       subroutine minmax_angles(x,y,z,r,n,ang,tab)
2225 !     When solutions do not exist, assume all angles
2226 !     are acceptable - i.e., initial geometry must be correct
2227 !      implicit none
2228
2229 !     Includes
2230 !      include 'COMMON.GEO'
2231 !      include 'COMMON.LOCMOVE'
2232
2233 !     Input arguments
2234       real(kind=8) :: x,y,z,r
2235
2236 !     Output arguments
2237       integer :: n
2238       real(kind=8),dimension(0:3) :: ang
2239       logical,dimension(0:2,0:3) :: tab
2240
2241 !     Local variables
2242       real(kind=8) :: num, denom, phi
2243       real(kind=8) :: Kmin, Kmax
2244       integer :: i
2245
2246
2247       num = x*x + y*y + z*z
2248       denom = x*x + y*y
2249       n = 0
2250       if (denom .gt. 0.) then
2251         phi = atan2(y,x)
2252         denom = 2.*r*sqrt(denom)
2253         num = num+r*r
2254         Kmin = (num - dmin2)/denom
2255         Kmax = (num - dmax2)/denom
2256
2257 !     Allowed values of K (else all angles are acceptable)
2258 !     -1 <= Kmin <  1
2259 !     -1 <  Kmax <= 1
2260         if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2261           Kmin = -flag
2262         else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2263           Kmin = PI
2264         else
2265           Kmin = acos(Kmin)
2266         endif
2267
2268         if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2269           Kmax = flag
2270         else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2271           Kmax = 0.
2272         else
2273           Kmax = acos(Kmax)
2274         endif
2275
2276         if (Kmax .lt. Kmin) Kmax = Kmin
2277
2278         call angles2tab(Kmin, Kmax, n, ang, tab)
2279
2280 !     Add phi and check that angles are within range (-PI,PI]
2281         do i=0,n-1
2282           ang(i) = ang(i)+phi
2283           if (ang(i) .le. -PI) then
2284             ang(i) = ang(i)+2.*PI
2285           else if (ang(i) .gt. PI) then
2286             ang(i) = ang(i)-2.*PI
2287           endif
2288         enddo
2289       endif
2290
2291       return
2292       end subroutine minmax_angles
2293 !-----------------------------------------------------------------------------
2294       subroutine construct_tab
2295 !     Take a_... and b_... values and produces the results res_...
2296 !     x_ang are assumed to be all different (diff > small)
2297 !     x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2298 !      implicit none
2299
2300 !     Includes
2301 !      include 'COMMON.LOCMOVE'
2302
2303 !     Local variables
2304       integer :: n_max,i,j,index
2305       logical :: done
2306       real(kind=8) :: phi
2307
2308
2309       n_max = a_n + b_n
2310       if (n_max .eq. 0) then
2311         res_n = 0
2312         return
2313       endif
2314
2315       do i=0,n_max-1
2316         do j=0,1
2317           res_tab(j,0,i) = .true.
2318           res_tab(j,2,i) = .true.
2319           res_tab(j,1,i) = .false.
2320         enddo
2321       enddo
2322
2323       index = 0
2324       phi = -flag
2325       done = .false.
2326       do while (.not.done)
2327         res_ang(index) = flag
2328
2329 !     Check a first...
2330         do i=0,a_n-1
2331           if ((a_ang(i)-phi).gt.small .and. &
2332                a_ang(i) .lt. res_ang(index)) then
2333 !     Found a lower angle
2334             res_ang(index) = a_ang(i)
2335 !     Copy the values from a_tab into res_tab(0,,)
2336             res_tab(0,0,index) = a_tab(0,i)
2337             res_tab(0,1,index) = a_tab(1,i)
2338             res_tab(0,2,index) = a_tab(2,i)
2339 !     Set default values for res_tab(1,,)
2340             res_tab(1,0,index) = .true.
2341             res_tab(1,1,index) = .false.
2342             res_tab(1,2,index) = .true.
2343           else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2344 !     Found an equal angle (can only be equal to a b_ang)
2345             res_tab(0,0,index) = a_tab(0,i)
2346             res_tab(0,1,index) = a_tab(1,i)
2347             res_tab(0,2,index) = a_tab(2,i)
2348           endif
2349         enddo
2350 !     ...then check b
2351         do i=0,b_n-1
2352           if ((b_ang(i)-phi).gt.small .and. &
2353                b_ang(i) .lt. res_ang(index)) then
2354 !     Found a lower angle
2355             res_ang(index) = b_ang(i)
2356 !     Copy the values from b_tab into res_tab(1,,)
2357             res_tab(1,0,index) = b_tab(0,i)
2358             res_tab(1,1,index) = b_tab(1,i)
2359             res_tab(1,2,index) = b_tab(2,i)
2360 !     Set default values for res_tab(0,,)
2361             res_tab(0,0,index) = .true.
2362             res_tab(0,1,index) = .false.
2363             res_tab(0,2,index) = .true.
2364           else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2365 !     Found an equal angle (can only be equal to an a_ang)
2366             res_tab(1,0,index) = b_tab(0,i)
2367             res_tab(1,1,index) = b_tab(1,i)
2368             res_tab(1,2,index) = b_tab(2,i)
2369           endif
2370         enddo
2371
2372         if (res_ang(index) .eq. flag) then
2373           res_n = index
2374           done = .true.
2375         else if (index .eq. n_max-1) then
2376           res_n = n_max
2377           done = .true.
2378         else
2379           phi = res_ang(index)  ! Store previous angle
2380           index = index+1
2381         endif
2382       enddo
2383
2384 !     Fill the gaps
2385 !     First a...
2386       index = 0
2387       if (a_n .gt. 0) then
2388         do while (.not.res_tab(0,1,index))
2389           index=index+1
2390         enddo
2391         done = res_tab(0,2,index)
2392         do i=index+1,res_n-1
2393           if (res_tab(0,1,i)) then
2394             done = res_tab(0,2,i)
2395           else
2396             res_tab(0,0,i) = done
2397             res_tab(0,1,i) = done
2398             res_tab(0,2,i) = done
2399           endif
2400         enddo
2401         done = res_tab(0,0,index)
2402         do i=index-1,0,-1
2403           if (res_tab(0,1,i)) then
2404             done = res_tab(0,0,i)
2405           else
2406             res_tab(0,0,i) = done
2407             res_tab(0,1,i) = done
2408             res_tab(0,2,i) = done
2409           endif
2410         enddo
2411       else
2412         do i=0,res_n-1
2413           res_tab(0,0,i) = .true.
2414           res_tab(0,1,i) = .true.
2415           res_tab(0,2,i) = .true.
2416         enddo
2417       endif
2418 !     ...then b
2419       index = 0
2420       if (b_n .gt. 0) then
2421         do while (.not.res_tab(1,1,index))
2422           index=index+1
2423         enddo
2424         done = res_tab(1,2,index)
2425         do i=index+1,res_n-1
2426           if (res_tab(1,1,i)) then
2427             done = res_tab(1,2,i)
2428           else
2429             res_tab(1,0,i) = done
2430             res_tab(1,1,i) = done
2431             res_tab(1,2,i) = done
2432           endif
2433         enddo
2434         done = res_tab(1,0,index)
2435         do i=index-1,0,-1
2436           if (res_tab(1,1,i)) then
2437             done = res_tab(1,0,i)
2438           else
2439             res_tab(1,0,i) = done
2440             res_tab(1,1,i) = done
2441             res_tab(1,2,i) = done
2442           endif
2443         enddo
2444       else
2445         do i=0,res_n-1
2446           res_tab(1,0,i) = .true.
2447           res_tab(1,1,i) = .true.
2448           res_tab(1,2,i) = .true.
2449         enddo
2450       endif
2451
2452 !     Finally fill the last row with AND operation
2453       do i=0,res_n-1
2454         do j=0,2
2455           res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2456         enddo
2457       enddo
2458
2459       return
2460       end subroutine construct_tab
2461 !-----------------------------------------------------------------------------
2462       subroutine construct_ranges(phi_n,phi_start,phi_end)
2463 !     Given the data in res_..., construct a table of
2464 !     min/max allowed angles
2465 !      implicit none
2466
2467 !     Includes
2468 !      include 'COMMON.GEO'
2469 !      include 'COMMON.LOCMOVE'
2470
2471 !     Output arguments
2472       integer :: phi_n
2473       real(kind=8),dimension(0:11) :: phi_start,phi_end
2474
2475 !     Local variables
2476       logical :: done
2477       integer :: index
2478
2479
2480       if (res_n .eq. 0) then
2481 !     Any move is allowed
2482         phi_n = 1
2483         phi_start(0) = -PI
2484         phi_end(0) = PI
2485       else
2486         phi_n = 0
2487         index = 0
2488         done = .false.
2489         do while (.not.done)
2490 !     Find start of range (01x)
2491           done = .false.
2492           do while (.not.done)
2493             if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2494               index=index+1
2495             else
2496               done = .true.
2497               phi_start(phi_n) = res_ang(index)
2498             endif
2499             if (index .eq. res_n) done = .true.
2500           enddo
2501 !     If a start was found (index < res_n), find the end of range (x10)
2502 !     It may not be found without wrapping around
2503           if (index .lt. res_n) then
2504             done = .false.
2505             do while (.not.done)
2506               if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2507                 index=index+1
2508               else
2509                 done = .true.
2510               endif
2511               if (index .eq. res_n) done = .true.
2512             enddo
2513             if (index .lt. res_n) then
2514 !     Found the end of the range
2515               phi_end(phi_n) = res_ang(index)
2516               phi_n=phi_n+1
2517               index=index+1
2518               if (index .eq. res_n) then
2519                 done = .true.
2520               else
2521                 done = .false.
2522               endif
2523             else
2524 !     Need to wrap around
2525               done = .true.
2526               phi_end(phi_n) = flag
2527             endif
2528           endif
2529         enddo
2530 !     Take care of the last one if need to wrap around
2531         if (phi_end(phi_n) .eq. flag) then
2532           index = 0
2533           do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2534             index=index+1
2535           enddo
2536           phi_end(phi_n) = res_ang(index) + 2.*PI
2537           phi_n=phi_n+1
2538         endif
2539       endif
2540
2541       return
2542       end subroutine construct_ranges
2543 !-----------------------------------------------------------------------------
2544       subroutine fix_no_moves(phi)
2545 !      implicit none
2546
2547 !     Includes
2548 !      include 'COMMON.GEO'
2549 !      include 'COMMON.LOCMOVE'
2550
2551 !     Output arguments
2552       real(kind=8) :: phi
2553
2554 !     Local variables
2555       integer :: index
2556       real(kind=8) :: diff,temp
2557
2558
2559 !     Look for first 01x in gammas (there MUST be at least one)
2560       diff = flag
2561       index = 0
2562       do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2563         index=index+1
2564       enddo
2565       if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2566 !     Try to increase PHImax
2567         if (index .gt. 0) then
2568           phi = res_ang(index-1)
2569           diff = abs(res_ang(index) - res_ang(index-1))
2570         endif
2571 !     Look for last (corresponding) x10
2572         index = res_n - 1
2573         do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2574           index=index-1
2575         enddo
2576         if (index .lt. res_n-1) then
2577           temp = abs(res_ang(index) - res_ang(index+1))
2578           if (temp .lt. diff) then
2579             phi = res_ang(index+1)
2580             diff = temp
2581           endif
2582         endif
2583       endif
2584
2585 !     If increasing PHImax didn't work, decreasing PHImin
2586 !     will (with one exception)
2587 !     Look for first x10 (there MUST be at least one)
2588       index = 0
2589       do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2590         index=index+1
2591       enddo
2592       if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2593 !     Try to decrease PHImin
2594         if (index .lt. res_n-1) then
2595           temp = abs(res_ang(index) - res_ang(index+1))
2596           if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2597             phi = res_ang(index+1)
2598             diff = temp
2599           endif
2600         endif
2601 !     Look for last (corresponding) 01x
2602         index = res_n - 1
2603         do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2604           index=index-1
2605         enddo
2606         if (index .gt. 0) then
2607           temp = abs(res_ang(index) - res_ang(index-1))
2608           if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2609             phi = res_ang(index-1)
2610             diff = temp
2611           endif
2612         endif
2613       endif
2614
2615 !     If it still didn't work, it must be PHImax == 0. or PHImin == PI
2616       if (diff .eq. flag) then
2617         index = 0
2618         if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2619              res_tab(index,1,2)) index = res_n - 1
2620 !     This MUST work at this point
2621         if (index .eq. 0) then
2622           phi = res_ang(1)
2623         else
2624           phi = res_ang(index - 1)
2625         endif
2626       endif
2627
2628       return
2629       end subroutine fix_no_moves
2630 !-----------------------------------------------------------------------------
2631       integer function move_res(PHImin,PHImax,i_move)
2632 !     Moves residue i_move (in array c), leaving everything else fixed
2633 !     Starting geometry is not checked, it should be correct!
2634 !     R(,i_move) is the only residue that will move, but must have
2635 !     1 < i_move < nres (i.e., cannot move ends)
2636 !     Whether any output is done is controlled by locmove_output
2637 !rc      implicit none
2638       use random,only:ran_number
2639 !     Includes
2640 !      implicit real*8 (a-h,o-z)
2641 !      include 'DIMENSIONS'
2642 !      include 'COMMON.CHAIN'
2643 !      include 'COMMON.GEO'
2644 !      include 'COMMON.LOCMOVE'
2645
2646 !     External functions
2647 !EL      double precision ran_number
2648 !EL      external ran_number
2649
2650 !     Input arguments
2651       real(kind=8) :: PHImin,PHImax
2652       integer :: i_move
2653
2654 !     RETURN VALUES:
2655 !     0: move successfull
2656 !     1: Dmin or Dmax had to be modified
2657 !     2: move failed - check your input geometry
2658
2659
2660 !     Local variables
2661       real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2662       real(kind=8),dimension(0:2) :: P
2663       logical :: no_moves,done
2664       integer :: index,i,j
2665       real(kind=8) :: phi,temp,radius
2666       real(kind=8),dimension(0:11) :: phi_start,phi_end
2667       integer :: phi_n
2668
2669 !     Set up the coordinate system
2670       do i=0,2
2671         Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2672       enddo
2673
2674       do i=0,2
2675         Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2676       enddo
2677       temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2678       do i=0,2
2679         Z(i)=Z(i)/temp
2680       enddo
2681
2682       do i=0,2
2683         X(i)=c(i+1,i_move)-Orig(i)
2684       enddo
2685 !     radius is the radius of the circle on which c(,i_move) can move
2686       radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2687       do i=0,2
2688         X(i)=X(i)/radius
2689       enddo
2690
2691       Y(0)=Z(1)*X(2)-X(1)*Z(2)
2692       Y(1)=X(0)*Z(2)-Z(0)*X(2)
2693       Y(2)=Z(0)*X(1)-X(0)*Z(1)
2694
2695 !     Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2696       if (i_move.gt.2) then
2697         do i=0,2
2698           P(i)=c(i+1,i_move-2)-Orig(i)
2699         enddo
2700         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2701              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2702              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2703              radius,a_n,a_ang,a_tab)
2704       else
2705         a_n=0
2706       endif
2707
2708 !     Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2709       if (i_move.lt.nres-2) then
2710         do i=0,2
2711           P(i)=c(i+1,i_move+2)-Orig(i)
2712         enddo
2713         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2714              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2715              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2716              radius,b_n,b_ang,b_tab)
2717       else
2718         b_n=0
2719       endif
2720
2721 !     Construct the resulting table for alpha and beta
2722       call construct_tab()
2723
2724       if (locmove_output) then
2725         print *,'ALPHAS & BETAS TABLE'
2726         call output_tabs()
2727       endif
2728
2729 !     Check that there is at least one possible move
2730       no_moves = .true.
2731       if (res_n .eq. 0) then
2732         no_moves = .false.
2733       else
2734         index = 0
2735         do while ((index .lt. res_n) .and. no_moves)
2736           if (res_tab(2,1,index)) no_moves = .false.
2737           index=index+1
2738         enddo
2739       endif
2740       if (no_moves) then
2741         if (locmove_output) print *,'   ***   Cannot move anywhere'
2742         move_res=2
2743         return
2744       endif
2745
2746 !     Transfer res_... into a_...
2747       a_n = 0
2748       do i=0,res_n-1
2749         if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2750              (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2751           a_ang(a_n) = res_ang(i)
2752           do j=0,2
2753             a_tab(j,a_n) = res_tab(2,j,i)
2754           enddo
2755           a_n=a_n+1
2756         endif
2757       enddo
2758
2759 !     Check that the PHI's are within [0,PI]
2760       if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2761       if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2762       if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2763       if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2764       if (PHImax .lt. PHImin) PHImax = PHImin
2765 !     Calculate min and max angles coming from PHImin and PHImax,
2766 !     and put them in b_...
2767       call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2768 !     Construct the final table
2769       call construct_tab()
2770
2771       if (locmove_output) then
2772         print *,'FINAL TABLE'
2773         call output_tabs()
2774       endif
2775
2776 !     Check that there is at least one possible move
2777       no_moves = .true.
2778       if (res_n .eq. 0) then
2779         no_moves = .false.
2780       else
2781         index = 0
2782         do while ((index .lt. res_n) .and. no_moves)
2783           if (res_tab(2,1,index)) no_moves = .false.
2784           index=index+1
2785         enddo
2786       endif
2787
2788       if (no_moves) then
2789 !     Take care of the case where no solution exists...
2790         call fix_no_moves(phi)
2791         if (locmove_output) then
2792           print *,'   ***   Had to modify PHImin or PHImax'
2793           print *,'phi: ',phi*rad2deg
2794         endif
2795         move_res=1
2796       else
2797 !     ...or calculate the solution
2798 !     Construct phi_start/phi_end arrays
2799         call construct_ranges(phi_n, phi_start, phi_end)
2800 !     Choose random angle phi in allowed range(s)
2801         temp = 0.
2802         do i=0,phi_n-1
2803           temp = temp + phi_end(i) - phi_start(i)
2804         enddo
2805         phi = ran_number(phi_start(0),phi_start(0)+temp)
2806         index = 0
2807         done = .false.
2808         do while (.not.done)
2809           if (phi .lt. phi_end(index)) then
2810             done = .true.
2811           else
2812             index=index+1
2813           endif
2814           if (index .eq. phi_n) then
2815             done = .true.
2816           else if (.not.done) then
2817             phi = phi + phi_start(index) - phi_end(index-1)
2818           endif
2819         enddo
2820         if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2821         if (phi .gt. PI) phi = phi-2.*PI
2822
2823         if (locmove_output) then
2824           print *,'ALLOWED RANGE(S)'
2825           do i=0,phi_n-1
2826             print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2827           enddo
2828           print *,'phi: ',phi*rad2deg
2829         endif
2830         move_res=0
2831       endif
2832
2833 !     Re-use radius as temp variable
2834       temp=radius*cos(phi)
2835       radius=radius*sin(phi)
2836       do i=0,2
2837         c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2838       enddo
2839
2840       return
2841       end function move_res
2842 !-----------------------------------------------------------------------------
2843       subroutine loc_test
2844 !rc      implicit none
2845
2846 !     Includes
2847 !      implicit real*8 (a-h,o-z)
2848 !      include 'DIMENSIONS'
2849 !      include 'COMMON.GEO'
2850 !      include 'COMMON.LOCAL'
2851 !      include 'COMMON.LOCMOVE'
2852
2853 !     External functions
2854 !EL      integer move_res
2855 !EL      external move_res
2856
2857 !     Local variables
2858       integer :: i,j,imov
2859       integer :: phi_n
2860       real(kind=8),dimension(0:11) :: phi_start,phi_end
2861       real(kind=8) :: phi
2862       real(kind=8),dimension(0:2,0:5) :: R
2863
2864       locmove_output=.true.
2865
2866 !      call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2867 !      call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2868 !      call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2869 !      call construct_tab
2870 !      call output_tabs
2871
2872 !      call construct_ranges(phi_n,phi_start,phi_end)
2873 !      do i=0,phi_n-1
2874 !        print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2875 !      enddo
2876
2877 !      call fix_no_moves(phi)
2878 !      print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2879
2880       R(0,0)=0.D0
2881       R(1,0)=0.D0
2882       R(2,0)=0.D0
2883       R(0,1)=0.D0
2884       R(1,1)=-cos(28.D0*deg2rad)
2885       R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2886       R(0,2)=0.D0
2887       R(1,2)=0.D0
2888       R(2,2)=-0.5D0
2889       R(0,3)=cos(30.D0*deg2rad)
2890       R(1,3)=0.D0
2891       R(2,3)=0.D0
2892       R(0,4)=0.D0
2893       R(1,4)=0.D0
2894       R(2,4)=0.5D0
2895       R(0,5)=0.D0
2896       R(1,5)=cos(26.D0*deg2rad)
2897       R(2,5)=0.5D0+sin(26.D0*deg2rad)
2898       do i=1,5
2899         do j=0,2
2900           R(j,i)=vbl*R(j,i)
2901         enddo
2902       enddo
2903 !      i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2904       imov=2
2905       i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2906       print *,'RETURNED ',i
2907       print *,(R(i,3)/vbl,i=0,2)
2908
2909       return
2910       end subroutine loc_test
2911 #endif
2912 !-----------------------------------------------------------------------------
2913 ! matmult.f
2914 !-----------------------------------------------------------------------------
2915       subroutine MATMULT(A1,A2,A3)
2916 !      implicit real*8 (a-h,o-z)
2917 !      include 'DIMENSIONS'
2918 !el local variables
2919       integer :: i,j,k
2920       real(kind=8) :: A3IJ
2921
2922       real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2923       real(kind=8),DIMENSION(3,3) :: AI3
2924       DO 1 I=1,3
2925         DO 2 J=1,3
2926           A3IJ=0.0
2927           DO 3 K=1,3
2928     3       A3IJ=A3IJ+A1(I,K)*A2(K,J)
2929           AI3(I,J)=A3IJ
2930     2   CONTINUE
2931     1 CONTINUE
2932       DO 4 I=1,3
2933       DO 4 J=1,3
2934     4   A3(I,J)=AI3(I,J)
2935       return
2936       end subroutine MATMULT
2937 !-----------------------------------------------------------------------------
2938 ! readpdb.F
2939 !-----------------------------------------------------------------------------
2940       subroutine int_from_cart(lside,lprn)
2941 !      implicit real*8 (a-h,o-z)
2942 !      include 'DIMENSIONS'
2943       use control_data,only:out1file
2944 #ifdef MPI
2945       include "mpif.h"
2946 #endif
2947 !      include 'COMMON.LOCAL'
2948 !      include 'COMMON.VAR'
2949 !      include 'COMMON.CHAIN'
2950 !      include 'COMMON.INTERACT'
2951 !      include 'COMMON.IOUNITS'
2952 !      include 'COMMON.GEO'
2953 !      include 'COMMON.NAMES'
2954 !      include 'COMMON.CONTROL'
2955 !      include 'COMMON.SETUP'
2956       character(len=3) :: seq,res
2957 !      character*5 atom
2958       character(len=80) :: card
2959       real(kind=8),dimension(3,20) :: sccor
2960       integer :: i,j,iti !el  rescode,
2961       logical :: lside,lprn
2962       real(kind=8) :: di,cosfac,sinfac
2963       integer :: nres2
2964       nres2=2*nres
2965
2966       if(me.eq.king.or..not.out1file)then
2967        if (lprn) then
2968         write (iout,'(/a)') &
2969         'Internal coordinates calculated from crystal structure.'
2970         if (lside) then
2971           write (iout,'(8a)') '  Res  ','       dvb','     Theta',&
2972        '     Gamma','    Dsc_id','       Dsc','     Alpha',&
2973        '     Beta '
2974         else
2975           write (iout,'(4a)') '  Res  ','       dvb','     Theta',&
2976        '     Gamma'
2977         endif
2978        endif
2979       endif
2980       do i=1,nres-1
2981 !       if (molnum(i).ne.1) cycle
2982 !in wham      do i=1,nres
2983         iti=itype(i,1)
2984         if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2985        (iti.ne.ntyp1  .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2986           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2987 !test          stop
2988         endif
2989 !#ifndef WHAM_RUN
2990         vbld(i+1)=dist(i,i+1)
2991         vbld_inv(i+1)=1.0d0/vbld(i+1)
2992 !#endif
2993         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2994         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2995       enddo
2996 !el -----
2997 !#ifdef WHAM_RUN
2998 !      if (itype(1,1).eq.ntyp1) then
2999 !        do j=1,3
3000 !          c(j,1)=c(j,2)+(c(j,3)-c(j,4))
3001 !        enddo
3002 !      endif
3003 !      if (itype(nres,1).eq.ntyp1) then
3004 !        do j=1,3
3005 !          c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
3006 !        enddo
3007 !      endif
3008 !#endif
3009 !      if (unres_pdb) then
3010 !        if (itype(1,1).eq.21) then
3011 !          theta(3)=90.0d0*deg2rad
3012 !          phi(4)=180.0d0*deg2rad
3013 !          vbld(2)=3.8d0
3014 !          vbld_inv(2)=1.0d0/vbld(2)
3015 !        endif
3016 !        if (itype(nres,1).eq.21) then
3017 !          theta(nres)=90.0d0*deg2rad
3018 !          phi(nres)=180.0d0*deg2rad
3019 !          vbld(nres)=3.8d0
3020 !          vbld_inv(nres)=1.0d0/vbld(2)
3021 !        endif
3022 !      endif
3023       if (lside) then
3024         do i=2,nres-1
3025           do j=1,3
3026             c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
3027            +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
3028 ! in wham            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
3029           enddo
3030           iti=itype(i,1)
3031           di=dist(i,nres+i)
3032 !#ifndef WHAM_RUN
3033 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3034
3035           if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3036            di=dsc(itype(i,molnum(i)))
3037           vbld(i+nres)=di
3038           if (itype(i,1).ne.10) then
3039             vbld_inv(i+nres)=1.0d0/di
3040           else
3041             vbld_inv(i+nres)=0.0d0
3042           endif
3043 !#endif
3044           if (iti.ne.10) then
3045             alph(i)=alpha(nres+i,i,nres2+2)
3046             omeg(i)=beta(nres+i,i,nres2+2,i+1)
3047           endif
3048           if (iti.ne.0) then
3049           if(me.eq.king.or..not.out1file)then
3050            if (lprn) &
3051            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3052            rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3053            rad2deg*alph(i),rad2deg*omeg(i)
3054           endif
3055           else
3056           if(me.eq.king.or..not.out1file)then
3057            if (lprn) &
3058            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3059            rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3060            rad2deg*alph(i),rad2deg*omeg(i)
3061           endif
3062           endif
3063         enddo
3064       else if (lprn) then
3065         do i=2,nres
3066           iti=itype(i,1)
3067           if(me.eq.king.or..not.out1file) &
3068            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3069            rad2deg*theta(i),rad2deg*phi(i)
3070         enddo
3071       endif
3072       return
3073       end subroutine int_from_cart
3074 !-----------------------------------------------------------------------------
3075       subroutine sc_loc_geom(lprn)
3076 !      implicit real*8 (a-h,o-z)
3077 !      include 'DIMENSIONS'
3078       use control_data,only:out1file
3079 #ifdef MPI
3080       include "mpif.h"
3081 #endif
3082 !      include 'COMMON.LOCAL'
3083 !      include 'COMMON.VAR'
3084 !      include 'COMMON.CHAIN'
3085 !      include 'COMMON.INTERACT'
3086 !      include 'COMMON.IOUNITS'
3087 !      include 'COMMON.GEO'
3088 !      include 'COMMON.NAMES'
3089 !      include 'COMMON.CONTROL'
3090 !      include 'COMMON.SETUP'
3091       real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3092       logical :: lprn
3093 !el local variables
3094       integer :: i,j,it,iti
3095       real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3096       do i=1,nres-1
3097         do j=1,3
3098           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3099         enddo
3100       enddo
3101       do i=2,nres-1
3102         if (itype(i,1).ne.10) then
3103           do j=1,3
3104             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3105           enddo
3106         else
3107           do j=1,3
3108             dc_norm(j,i+nres)=0.0d0
3109           enddo
3110         endif
3111       enddo
3112       do i=2,nres-1
3113         costtab(i+1) =dcos(theta(i+1))
3114         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3115         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3116         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3117         cosfac2=0.5d0/(1.0d0+costtab(i+1))
3118         cosfac=dsqrt(cosfac2)
3119         sinfac2=0.5d0/(1.0d0-costtab(i+1))
3120         sinfac=dsqrt(sinfac2)
3121         it=itype(i,1)
3122
3123         if ((it.ne.10).and.(it.ne.ntyp1)) then
3124 !el        if (it.ne.10) then
3125 !
3126 !  Compute the axes of tghe local cartesian coordinates system; store in
3127 !   x_prime, y_prime and z_prime
3128 !
3129         do j=1,3
3130           x_prime(j) = 0.00
3131           y_prime(j) = 0.00
3132           z_prime(j) = 0.00
3133         enddo
3134         do j = 1,3
3135           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3136           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3137         enddo
3138         call vecpr(x_prime,y_prime,z_prime)
3139 !
3140 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3141 ! to local coordinate system. Store in xx, yy, zz.
3142 !
3143         xx=0.0d0
3144         yy=0.0d0
3145         zz=0.0d0
3146         do j = 1,3
3147           xx = xx + x_prime(j)*dc_norm(j,i+nres)
3148           yy = yy + y_prime(j)*dc_norm(j,i+nres)
3149           zz = zz + z_prime(j)*dc_norm(j,i+nres)
3150         enddo
3151
3152         xxref(i)=xx
3153         yyref(i)=yy
3154         zzref(i)=zz
3155         else
3156         xxref(i)=0.0d0
3157         yyref(i)=0.0d0
3158         zzref(i)=0.0d0
3159         endif
3160       enddo
3161       if (lprn) then
3162         do i=2,nres
3163           iti=itype(i,1)
3164           if(me.eq.king.or..not.out1file) &
3165            write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3166             yyref(i),zzref(i)
3167         enddo
3168       endif
3169
3170       return
3171       end subroutine sc_loc_geom
3172 !-----------------------------------------------------------------------------
3173       subroutine sccenter(ires,nscat,sccor)
3174 !      implicit real*8 (a-h,o-z)
3175 !      include 'DIMENSIONS'
3176 !      include 'COMMON.CHAIN'
3177       integer :: i,j,ires,nscat
3178       real(kind=8),dimension(3,20) :: sccor
3179       real(kind=8) :: sccmj
3180 !        print *,"I am in sccenter",ires,nscat
3181       do j=1,3
3182         sccmj=0.0D0
3183         do i=1,nscat
3184           sccmj=sccmj+sccor(j,i)
3185 !C          print *,"insccent", ires,sccor(j,i)
3186         enddo
3187         dc(j,ires)=sccmj/nscat
3188       enddo
3189       return
3190       end subroutine sccenter
3191 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3192 !-----------------------------------------------------------------------------
3193       subroutine bond_regular
3194       use calc_data
3195 !      implicit real*8 (a-h,o-z)
3196 !      include 'DIMENSIONS'
3197 !      include 'COMMON.VAR'
3198 !      include 'COMMON.LOCAL'
3199 !      include 'COMMON.CALC'
3200 !      include 'COMMON.INTERACT'
3201 !      include 'COMMON.CHAIN'
3202       do i=1,nres-1
3203
3204        vbld(i+1)=vbl
3205        vbld_inv(i+1)=1.0d0/vbld(i+1)
3206        vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3207        vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3208 !       print *,vbld(i+1),vbld(i+1+nres)
3209       enddo
3210       return
3211       end subroutine bond_regular
3212 #endif
3213 !-----------------------------------------------------------------------------
3214 ! refsys.f
3215 !-----------------------------------------------------------------------------
3216       subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3217 ! This subroutine calculates unit vectors of a local reference system
3218 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3219 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3220 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3221 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3222 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3223 ! form a linear fragment. Returns vectors e1, e2, and e3.
3224 !      implicit real*8 (a-h,o-z)
3225 !      include 'DIMENSIONS'
3226       logical :: fail
3227       real(kind=8),dimension(3) :: e1,e2,e3
3228       real(kind=8),dimension(3) :: u,z
3229 !      include 'COMMON.IOUNITS'
3230 !      include 'COMMON.CHAIN'
3231       real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3232 !el local variables
3233       integer :: i,i1,i2,i3,i4
3234       real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3235       fail=.false.
3236       s1=0.0
3237       s2=0.0
3238       do 1 i=1,3
3239       zi=c(i,i2)-c(i,i3)
3240       ui=c(i,i4)-c(i,i3)
3241       s1=s1+zi*zi
3242       s2=s2+ui*ui
3243       z(i)=zi
3244     1 u(i)=ui
3245       s1=sqrt(s1)
3246       s2=sqrt(s2)
3247       if (s1.gt.coinc) goto 2
3248       write (iout,1000) i2,i3,i1
3249       fail=.true.
3250 !     do 3 i=1,3
3251 !   3 c(i,i1)=0.0D0
3252       return
3253     2 if (s2.gt.coinc) goto 4
3254       write(iout,1000) i3,i4,i1
3255       fail=.true.
3256       do 5 i=1,3
3257     5 c(i,i1)=0.0D0
3258       return
3259     4 s1=1.0/s1
3260       s2=1.0/s2
3261       v1=z(2)*u(3)-z(3)*u(2)
3262       v2=z(3)*u(1)-z(1)*u(3)
3263       v3=z(1)*u(2)-z(2)*u(1)
3264       anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3265       if (anorm.gt.align) goto 6
3266       write (iout,1010) i2,i3,i4,i1
3267       fail=.true.
3268 !     do 7 i=1,3
3269 !   7 c(i,i1)=0.0D0
3270       return
3271     6 anorm=1.0D0/anorm
3272       e3(1)=v1*anorm
3273       e3(2)=v2*anorm
3274       e3(3)=v3*anorm
3275       e1(1)=z(1)*s1
3276       e1(2)=z(2)*s1
3277       e1(3)=z(3)*s1
3278       e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3279       e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3280       e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3281  1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3282        'coordinates of atom',i4,' are set to zero.')
3283  1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3284        ' fragment. coordinates of atom',i4,' are set to zero.')
3285       return
3286       end subroutine refsys
3287 !-----------------------------------------------------------------------------
3288 ! int_to_cart.f
3289 !-----------------------------------------------------------------------------
3290       subroutine int_to_cart
3291 !--------------------------------------------------------------
3292 !  This subroutine converts the energy derivatives from internal
3293 !  coordinates to cartesian coordinates
3294 !-------------------------------------------------------------
3295 !      implicit real*8 (a-h,o-z)
3296 !      include 'DIMENSIONS'
3297 !      include 'COMMON.VAR'
3298 !      include 'COMMON.CHAIN'
3299 !      include 'COMMON.DERIV'
3300 !      include 'COMMON.GEO'
3301 !      include 'COMMON.LOCAL'
3302 !      include 'COMMON.INTERACT'
3303 !      include 'COMMON.MD'
3304 !      include 'COMMON.IOUNITS'
3305 !      include 'COMMON.SCCOR'
3306 !   calculating dE/ddc1
3307 !el local variables
3308        integer :: j,i
3309 !       print *,"gloc",gloc(:,:)
3310 !       print *, "gcart",gcart(:,:)
3311        if (nres.lt.3) go to 18
3312        do j=1,3
3313          gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3314            +gloc(nres-2,icg)*dtheta(j,1,3)
3315           if ((itype(2,1).ne.10).and.&
3316           (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3317           gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3318           gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3319         endif
3320        enddo
3321 !     Calculating the remainder of dE/ddc2
3322        do j=1,3
3323          gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3324          gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3325         if(itype(2,1).ne.10) then
3326           gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3327           gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3328         endif
3329         if(itype(3,1).ne.10) then
3330           gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3331           gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3332         endif
3333         if(nres.gt.4) then
3334           gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3335         endif
3336        enddo
3337 !  If there are only five residues
3338        if(nres.eq.5) then
3339          do j=1,3
3340            gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3341            dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3342            dtheta(j,1,5)
3343 !         if(itype(3,1).ne.10) then
3344           if ((itype(3,1).ne.10).and.&
3345           (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3346            gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3347            dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3348          endif
3349 !        if(itype(4,1).ne.10) then
3350           if ((itype(4,1).ne.10).and.&
3351           (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3352            gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3353            dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3354          endif
3355         enddo
3356        endif
3357 !    If there are more than five residues
3358       if(nres.gt.5) then
3359         do i=3,nres-3
3360          do j=1,3
3361           gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3362           +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3363           gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3364           gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3365           if(itype(i,1).ne.10) then
3366            gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3367            gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3368           endif
3369           if(itype(i+1,1).ne.10) then
3370            gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3371            +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3372           endif
3373          enddo
3374         enddo
3375       endif
3376 !  Setting dE/ddnres-2
3377       if(nres.gt.5) then
3378          do j=1,3
3379            gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3380            dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3381            +gloc(2*nres-6,icg)* &
3382            dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3383           if(itype(nres-2,1).ne.10) then
3384               gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3385               dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3386               domega(j,2,nres-2)
3387           endif
3388           if(itype(nres-1,1).ne.10) then
3389              gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3390              dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3391              domega(j,1,nres-1)
3392           endif
3393          enddo
3394       endif
3395 !  Settind dE/ddnres-1
3396 !#define DEBUG
3397 #ifdef DEBUG
3398           j=1
3399               write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3400         gloc(2*nres-5,icg),dtheta(j,2,nres)
3401
3402 #endif
3403 !#undef DEBUG
3404
3405        do j=1,3
3406         gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3407         gloc(2*nres-5,icg)*dtheta(j,2,nres)
3408 !#define DEBUG
3409 #ifdef DEBUG
3410               write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3411         gloc(2*nres-5,icg),dtheta(j,2,nres)
3412
3413 #endif
3414 !#undef DEBUG
3415         if(itype(nres-1,1).ne.10) then
3416           gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3417           dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3418           domega(j,2,nres-1)
3419 !#define DEBUG
3420 #ifdef DEBUG
3421               write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3422           dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3423           domega(j,2,nres-1)
3424
3425 #endif
3426 !#undef DEBUG
3427
3428         endif
3429         enddo
3430 !   The side-chain vector derivatives
3431         do i=2,nres-1
3432          if(itype(i,1).ne.10 .and.  &
3433            itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3434             do j=1,3
3435               gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3436               +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3437 !#define DEBUG
3438 #ifdef DEBUG
3439               write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3440               gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3441 #endif
3442 !#undef DEBUG
3443             enddo
3444          endif
3445        enddo
3446 !----------------------------------------------------------------------
3447 ! INTERTYP=1 SC...Ca...Ca...Ca
3448 ! INTERTYP=2 Ca...Ca...Ca...SC
3449 ! INTERTYP=3 SC...Ca...Ca...SC
3450 !   calculating dE/ddc1
3451   18   continue
3452 !       do i=1,nres
3453 !       gloc(i,icg)=0.0D0
3454 !          write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3455 !       enddo
3456        if (nres.lt.2) return
3457        if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3458        if ((itype(1,1).ne.10).and. &
3459         (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3460         do j=1,3
3461 !c Derviative was calculated for oposite vector of side chain therefore
3462 ! there is "-" sign before gloc_sc
3463          gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3464            dtauangle(j,1,1,3)
3465          gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3466            dtauangle(j,1,2,3)
3467           if ((itype(2,1).ne.10).and. &
3468         (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3469          gxcart(j,1)= gxcart(j,1) &
3470                      -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3471          gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3472             dtauangle(j,3,2,3)
3473           endif
3474        enddo
3475        endif
3476          if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3477          (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3478       then
3479          do j=1,3
3480          gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3481          enddo
3482          endif
3483 !   As potetnial DO NOT depend on omicron anlge their derivative is
3484 !   ommited
3485 !     &     +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3486
3487 !     Calculating the remainder of dE/ddc2
3488        do j=1,3
3489          if((itype(2,1).ne.10).and. &
3490            (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3491            if ((itype(1,1).ne.10).and.&
3492               ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3493             gxcart(j,2)=gxcart(j,2)+ &
3494                                gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3495         if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3496          then
3497            gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3498 !c                  the   - above is due to different vector direction
3499            gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3500           endif
3501           if (nres.gt.3) then
3502 !           if ((itype(1,1).ne.10).and.&
3503 !              ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3504            gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3505 !c                  the   - above is due to different vector direction
3506            gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3507 !          write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3508 !           write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3509           endif
3510          endif
3511          if ((itype(1,1).ne.10).and.&
3512          (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3513           gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3514 !           write(iout,*)  gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3515         endif
3516          if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3517           gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3518 !           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3519          endif
3520          if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3521           gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3522 !           write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3523          endif
3524
3525 !      write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3526        enddo
3527 !    If there are more than five residues
3528       if(nres.ge.5) then
3529         do i=3,nres-2
3530          do j=1,3
3531 !          write(iout,*) "before", gcart(j,i)
3532           if ((itype(i,1).ne.10).and.&
3533           (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3534           gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3535           *dtauangle(j,2,3,i+1) &
3536           -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3537           gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3538           *dtauangle(j,1,2,i+2)
3539 !                   write(iout,*) "new",j,i,
3540 !     &  gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3541 !          if (itype(i-1,1).ne.10) then
3542           if ((itype(i-1,1).ne.10).and.&
3543           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3544
3545            gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3546       *dtauangle(j,3,3,i+1)
3547           endif
3548 !          if (itype(i+1,1).ne.10) then
3549           if ((itype(i+1,1).ne.10).and.&
3550           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3551           gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3552       *dtauangle(j,3,1,i+2)
3553            gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3554       *dtauangle(j,3,2,i+2)
3555           endif
3556           endif
3557 !          if (itype(i-1,1).ne.10) then
3558           if ((itype(i-1,1).ne.10).and.&
3559           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3560            gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3561            dtauangle(j,1,3,i+1)
3562           endif
3563 !          if (itype(i+1,1).ne.10) then
3564           if ((itype(i+1,1).ne.10).and.&
3565           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3566            gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3567            dtauangle(j,2,2,i+2)
3568 !          write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3569 !     &    dtauangle(j,2,2,i+2)
3570           endif
3571 !          if (itype(i+2,1).ne.10) then
3572           if ((itype(i+2,1).ne.10).and.&
3573           (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3574            gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3575            dtauangle(j,2,1,i+3)
3576           endif
3577          enddo
3578         enddo
3579       endif
3580 !  Setting dE/ddnres-1
3581       if(nres.ge.4) then
3582          do j=1,3
3583          if ((itype(nres-1,1).ne.10).and.&
3584        (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3585          gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3586           *dtauangle(j,2,3,nres)
3587 !          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3588 !     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
3589 !         if (itype(nres-2,1).ne.10) then
3590          if ((itype(nres-2,1).ne.10).and.&
3591        (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3592        gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3593           *dtauangle(j,3,3,nres)
3594           endif
3595          if ((itype(nres,1).ne.10).and.&
3596          (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3597         gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3598           *dtauangle(j,3,1,nres+1)
3599         gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3600           *dtauangle(j,3,2,nres+1)
3601           endif
3602          endif
3603          if ((itype(nres-2,1).ne.10).and.&
3604          (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3605             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3606          dtauangle(j,1,3,nres)
3607          endif
3608           if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3609             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3610            dtauangle(j,2,2,nres+1)
3611 !           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3612 !     &     dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3613            endif
3614          enddo
3615       endif
3616 !  Settind dE/ddnres
3617        if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3618           (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3619        do j=1,3
3620         gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3621        *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3622        *dtauangle(j,2,3,nres+1)
3623         enddo
3624        endif
3625 !   The side-chain vector derivatives
3626 !       print *,"gcart",gcart(:,:)
3627       return
3628       end subroutine int_to_cart
3629 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3630 !-----------------------------------------------------------------------------
3631 ! readrtns_CSA.F
3632 !-----------------------------------------------------------------------------
3633       subroutine gen_dist_constr
3634 ! Generate CA distance constraints.
3635 !      implicit real*8 (a-h,o-z)
3636 !      include 'DIMENSIONS'
3637 !      include 'COMMON.IOUNITS'
3638 !      include 'COMMON.GEO'
3639 !      include 'COMMON.VAR'
3640 !      include 'COMMON.INTERACT'
3641 !      include 'COMMON.LOCAL'
3642 !      include 'COMMON.NAMES'
3643 !      include 'COMMON.CHAIN'
3644 !      include 'COMMON.FFIELD'
3645 !      include 'COMMON.SBRIDGE'
3646 !      include 'COMMON.HEADER'
3647 !      include 'COMMON.CONTROL'
3648 !      include 'COMMON.DBASE'
3649 !      include 'COMMON.THREAD'
3650 !      include 'COMMON.TIME1'
3651 !      integer :: itype_pdb !(maxres)
3652 !      common /pizda/ itype_pdb(nres)
3653       character(len=2) :: iden
3654 !el local variables
3655       integer :: i,j
3656 !d      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3657 !d      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3658 !d     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3659 !d     & ' nsup',nsup
3660       do i=nstart_sup,nstart_sup+nsup-1
3661 !d      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3662 !d     &    ' seq_pdb', restyp(itype_pdb(i))
3663         do j=i+2,nstart_sup+nsup-1
3664           nhpb=nhpb+1
3665           ihpb(nhpb)=i+nstart_seq-nstart_sup
3666           jhpb(nhpb)=j+nstart_seq-nstart_sup
3667           forcon(nhpb)=weidis
3668           dhpb(nhpb)=dist(i,j)
3669         enddo
3670       enddo
3671 !d      write (iout,'(a)') 'Distance constraints:'
3672 !d      do i=nss+1,nhpb
3673 !d        ii=ihpb(i)
3674 !d        jj=jhpb(i)
3675 !d        iden='CA'
3676 !d        if (ii.gt.nres) then
3677 !d          iden='SC'
3678 !d          ii=ii-nres
3679 !d          jj=jj-nres
3680 !d        endif
3681 !d        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3682 !d     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3683 !d     &  dhpb(i),forcon(i)
3684 !d      enddo
3685 !      deallocate(itype_pdb)
3686
3687       return
3688       end subroutine gen_dist_constr
3689 #endif
3690 !-----------------------------------------------------------------------------
3691 ! cartprint.f
3692 !-----------------------------------------------------------------------------
3693       subroutine cartprint
3694
3695       use geometry_data, only: c
3696       use energy_data, only: itype
3697 !      implicit real*8 (a-h,o-z)
3698 !      include 'DIMENSIONS'
3699 !      include 'COMMON.CHAIN'
3700 !      include 'COMMON.INTERACT'
3701 !      include 'COMMON.NAMES'
3702 !      include 'COMMON.IOUNITS'
3703       integer :: i
3704
3705       write (iout,100)
3706       do i=1,nres
3707         write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3708           c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3709       enddo
3710   100 format (//'              alpha-carbon coordinates       ',&
3711                 '     centroid coordinates'/ &
3712                 '       ', 6X,'X',11X,'Y',11X,'Z',&
3713                                 10X,'X',11X,'Y',11X,'Z')
3714   110 format (a,'(',i3,')',6f12.5)
3715       return
3716       end subroutine cartprint
3717 !-----------------------------------------------------------------------------
3718 !-----------------------------------------------------------------------------
3719       subroutine alloc_geo_arrays
3720 !EL Allocation of tables used by module energy
3721
3722       integer :: i,j,nres2
3723       nres2=2*nres
3724 ! commom.bounds
3725 !      common /bounds/
3726       allocate(phibound(2,nres+2)) !(2,maxres)
3727 !----------------------
3728 ! commom.chain
3729 !      common /chain/ in molread
3730 !      real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3731 !      real(kind=8),dimension(:,:),allocatable :: dc
3732       allocate(dc_old(3,0:nres2))
3733 !      if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3734       if(.not.allocated(dc_norm2)) then
3735         allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3736         dc_norm2(:,:)=0.d0
3737       endif
3738 !
3739 !el      if(.not.allocated(dc_norm))
3740 !elwrite(iout,*) "jestem w alloc geo 1"
3741       if(.not.allocated(dc_norm)) then
3742         allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3743         dc_norm(:,:)=0.d0
3744       endif
3745 !elwrite(iout,*) "jestem w alloc geo 1"
3746       allocate(xloc(3,nres),xrot(3,nres))
3747 !elwrite(iout,*) "jestem w alloc geo 1"
3748       xloc(:,:)=0.0D0
3749 !elwrite(iout,*) "jestem w alloc geo 1"
3750       allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3751 !      common /rotmat/
3752       allocate(t(3,3,nres),r(3,3,nres))
3753       allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3754 !      common /refstruct/
3755       if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3756 !elwrite(iout,*) "jestem w alloc geo 2"
3757       allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3758       if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3759       if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3760 !      common /from_zscore/ in module.compare
3761 !----------------------
3762 ! common.local
3763 ! Inverses of the actual virtual bond lengths
3764 !      common /invlen/ in io_conf: molread or readpdb
3765 !      real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3766 !----------------------
3767 ! common.var
3768 ! Store the geometric variables in the following COMMON block.
3769 !      common /var/ in readpdb or ...
3770       if(.not.allocated(theta)) allocate(theta(nres+2))
3771       if(.not.allocated(phi)) allocate(phi(nres+2))
3772       if(.not.allocated(alph)) allocate(alph(nres+2))
3773       if(.not.allocated(omeg)) allocate(omeg(nres+2))
3774       if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3775       if(.not.allocated(phiref)) allocate(phiref(nres+2))
3776       if(.not.allocated(costtab)) allocate(costtab(nres))
3777       if(.not.allocated(sinttab)) allocate(sinttab(nres))
3778       if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3779       if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3780 !      real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3781       allocate(omicron(2,nres+2)) !(2,maxres)
3782       allocate(tauangle(3,nres+2)) !(3,maxres)
3783 !elwrite(iout,*) "jestem w alloc geo 3"
3784       if(.not.allocated(xxtab)) allocate(xxtab(nres))
3785       if(.not.allocated(yytab)) allocate(yytab(nres))
3786       if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3787       if(.not.allocated(xxref)) allocate(xxref(nres))
3788       if(.not.allocated(yyref)) allocate(yyref(nres))
3789       if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3790       allocate(ialph(nres,2)) !(maxres,2)
3791       ialph(:,1)=0
3792       ialph(:,2)=0
3793       allocate(ivar(4*nres2)) !(4*maxres2)
3794
3795 #if defined(WHAM_RUN) || defined(CLUSTER)
3796       allocate(vbld(2*nres))
3797       vbld(:)=0.d0
3798       allocate(vbld_inv(2*nres))
3799       vbld_inv(:)=0.d0
3800 #endif
3801
3802       return
3803       end subroutine alloc_geo_arrays
3804 !-----------------------------------------------------------------------------
3805 !-----------------------------------------------------------------------------
3806       subroutine returnbox
3807       integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3808       integer :: chain_end,ireturnval
3809       real*8 :: difference
3810 !C change suggested by Ana - end
3811         j=1
3812         chain_beg=1
3813 !C        do i=1,nres
3814 !C       write(*,*) 'initial', i,j,c(j,i)
3815 !C        enddo
3816 !C change suggested by Ana - begin
3817         allareout=1
3818 !C change suggested by Ana -end
3819         do i=1,nres-1
3820            mnum=molnum(i)
3821          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3822             .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3823           chain_end=i
3824           if (allareout.eq.1) then
3825             ireturnval=int(c(j,i)/boxxsize)
3826             if (c(j,i).le.0) ireturnval=ireturnval-1
3827             do k=chain_beg,chain_end
3828               c(j,k)=c(j,k)-ireturnval*boxxsize
3829               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3830             enddo
3831 !C Suggested by Ana
3832             if (chain_beg.eq.1) &
3833             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3834 !C Suggested by Ana -end
3835            endif
3836            chain_beg=i+1
3837            allareout=1
3838          else
3839           if (int(c(j,i)/boxxsize).eq.0) allareout=0
3840          endif
3841         enddo
3842          if (allareout.eq.1) then
3843             ireturnval=int(c(j,i)/boxxsize)
3844             if (c(j,i).le.0) ireturnval=ireturnval-1
3845             do k=chain_beg,nres
3846               c(j,k)=c(j,k)-ireturnval*boxxsize
3847               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3848             enddo
3849           endif
3850 !C NO JUMP
3851 !C        do i=1,nres
3852 !C        write(*,*) 'befor no jump', i,j,c(j,i)
3853 !C        enddo
3854         nojumpval=0
3855         do i=2,nres
3856            mnum=molnum(i)
3857            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3858               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3859              difference=abs(c(j,i-1)-c(j,i))
3860 !C             print *,'diff', difference
3861              if (difference.gt.boxxsize/2.0) then
3862                 if (c(j,i-1).gt.c(j,i)) then
3863                   nojumpval=1
3864                  else
3865                    nojumpval=-1
3866                  endif
3867               else
3868               nojumpval=0
3869               endif
3870               endif
3871               c(j,i)=c(j,i)+nojumpval*boxxsize
3872               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3873          enddo
3874        nojumpval=0
3875         do i=2,nres
3876            mnum=molnum(i)
3877            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3878              difference=abs(c(j,i-1)-c(j,i))
3879              if (difference.gt.boxxsize/2.0) then
3880                 if (c(j,i-1).gt.c(j,i)) then
3881                   nojumpval=1
3882                  else
3883                    nojumpval=-1
3884                  endif
3885               else
3886               nojumpval=0
3887               endif
3888              endif
3889               c(j,i)=c(j,i)+nojumpval*boxxsize
3890               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3891          enddo
3892
3893 !C        do i=1,nres
3894 !C        write(*,*) 'after no jump', i,j,c(j,i)
3895 !C        enddo
3896
3897 !C NOW Y dimension
3898 !C suggesed by Ana begins
3899         allareout=1
3900         j=2
3901         chain_beg=1
3902         do i=1,nres-1
3903            mnum=molnum(i)
3904          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3905            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3906           chain_end=i
3907           if (allareout.eq.1) then
3908             ireturnval=int(c(j,i)/boxysize)
3909             if (c(j,i).le.0) ireturnval=ireturnval-1
3910             do k=chain_beg,chain_end
3911               c(j,k)=c(j,k)-ireturnval*boxysize
3912              c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3913             enddo
3914 !C Suggested by Ana
3915             if (chain_beg.eq.1) &
3916             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3917 !C Suggested by Ana -end
3918            endif
3919            chain_beg=i+1
3920            allareout=1
3921          else
3922           if (int(c(j,i)/boxysize).eq.0) allareout=0
3923          endif
3924         enddo
3925          if (allareout.eq.1) then
3926             ireturnval=int(c(j,i)/boxysize)
3927             if (c(j,i).le.0) ireturnval=ireturnval-1
3928             do k=chain_beg,nres
3929               c(j,k)=c(j,k)-ireturnval*boxysize
3930               c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3931             enddo
3932           endif
3933         nojumpval=0
3934         do i=2,nres
3935            mnum=molnum(i)
3936            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3937               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3938              difference=abs(c(j,i-1)-c(j,i))
3939              if (difference.gt.boxysize/2.0) then
3940                 if (c(j,i-1).gt.c(j,i)) then
3941                   nojumpval=1
3942                  else
3943                    nojumpval=-1
3944                  endif
3945              else
3946               nojumpval=0
3947               endif
3948            endif
3949               c(j,i)=c(j,i)+nojumpval*boxysize
3950               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3951          enddo
3952       nojumpval=0
3953         do i=2,nres
3954            mnum=molnum(i)
3955            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3956              .and. itype(i-1,mnum).eq.ntyp1) then
3957              difference=abs(c(j,i-1)-c(j,i))
3958              if (difference.gt.boxysize/2.0) then
3959                 if (c(j,i-1).gt.c(j,i)) then
3960                   nojumpval=1
3961                  else
3962                    nojumpval=-1
3963                  endif
3964               else
3965               nojumpval=0
3966               endif
3967             endif
3968               c(j,i)=c(j,i)+nojumpval*boxysize
3969               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3970          enddo
3971 !C Now Z dimension
3972 !C Suggested by Ana -begins
3973         allareout=1
3974 !C Suggested by Ana -ends
3975        j=3
3976         chain_beg=1
3977         do i=1,nres-1
3978            mnum=molnum(i)
3979          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3980            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3981           chain_end=i
3982           if (allareout.eq.1) then
3983             ireturnval=int(c(j,i)/boxysize)
3984             if (c(j,i).le.0) ireturnval=ireturnval-1
3985             do k=chain_beg,chain_end
3986               c(j,k)=c(j,k)-ireturnval*boxzsize
3987               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3988             enddo
3989 !C Suggested by Ana
3990             if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3991 !C Suggested by Ana -end
3992            endif
3993            chain_beg=i+1
3994            allareout=1
3995          else
3996           if (int(c(j,i)/boxzsize).eq.0) allareout=0
3997          endif
3998         enddo
3999          if (allareout.eq.1) then
4000             ireturnval=int(c(j,i)/boxzsize)
4001             if (c(j,i).le.0) ireturnval=ireturnval-1
4002             do k=chain_beg,nres
4003               c(j,k)=c(j,k)-ireturnval*boxzsize
4004               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
4005             enddo
4006           endif
4007         nojumpval=0
4008         do i=2,nres
4009            mnum=molnum(i)
4010            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4011              difference=abs(c(j,i-1)-c(j,i))
4012              if (difference.gt.(boxzsize/2.0)) then
4013                 if (c(j,i-1).gt.c(j,i)) then
4014                   nojumpval=1
4015                  else
4016                    nojumpval=-1
4017                  endif
4018               else
4019               nojumpval=0
4020               endif
4021             endif
4022               c(j,i)=c(j,i)+nojumpval*boxzsize
4023               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4024          enddo
4025        nojumpval=0
4026         do i=2,nres
4027            mnum=molnum(i)
4028            if (itype(i,mnum).eq.ntyp1_molec(mnum) &
4029             .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4030              difference=abs(c(j,i-1)-c(j,i))
4031              if (difference.gt.boxzsize/2.0) then
4032                 if (c(j,i-1).gt.c(j,i)) then
4033                   nojumpval=1
4034                  else
4035                    nojumpval=-1
4036                  endif
4037               else
4038               nojumpval=0
4039               endif
4040             endif
4041              c(j,i)=c(j,i)+nojumpval*boxzsize
4042               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4043          enddo
4044         do i=1,nres
4045          if (molnum(i).eq.5) then
4046           c(1,i)=dmod(c(1,i),boxxsize)
4047           c(2,i)=dmod(c(2,i),boxysize)
4048           c(3,i)=dmod(c(3,i),boxzsize)
4049           c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4050           c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4051           c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4052          endif
4053         enddo
4054         return
4055         end       subroutine returnbox
4056 !-------------------------------------------------------------------------------------------------------
4057       end module geometry