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         call orig_frame
 849         i=4
 850         nstart=4
 851       else
 852         i=nstart
 853         nstart=max0(i,4)
 854       endif
 855
 856       maxnit=0
 857
 858       nit=0
 859       niter=0
 860       back=.false.
 861       do while (i.le.nres .and. niter.lt.maxgen)
 862         write(iout,*) 'i=',i,'back=',back
 863         if (i.lt.nstart) then
 864           if(iprint.gt.1) then
 865           write (iout,'(/80(1h*)/2a/80(1h*))') &
 866                 'Generation procedure went down to ',&
 867                 'chain beginning. Cannot continue...'
 868           write (*,'(/80(1h*)/2a/80(1h*))') &
 869                 'Generation procedure went down to ',&
 870                 'chain beginning. Cannot continue...'
 871           endif
 872           return 1
 873         endif
 874         it1=iabs(itype(i-1,molnum(i-1)))
 875         it2=iabs(itype(i-2,molnum(i-2)))
 876         it=iabs(itype(i,molnum(i)))
 877         if ((it.eq.ntyp1).and.(it1.eq.ntyp1)) &
 878           vbld(i)=ran_number(30.0D0,40.0D0)
 879 !       print *,'Gen_Rand_Conf: i=',i,' it=',it,' it1=',it1,' it2=',it2,&
 880 !        ' nit=',nit,' niter=',niter,' maxgen=',maxgen
 881         phi(i+1)=gen_phi(i+1,it1,it)
 882         if (back) then
 883           phi(i)=gen_phi(i+1,it2,it1)
 884 !         print *,'phi(',i,')=',phi(i)
 885           theta(i-1)=gen_theta(it2,phi(i-1),phi(i),molnum(i))
 886 !          print *,"theta",theta(i-1),phi(i)
 887           if ((it2.ne.10).and.(it2.ne.ntyp1)) then
 888             nsi=0
 889             fail=.true.
 890             do while (fail.and.nsi.le.maxsi)
 891               call gen_side(it2,theta(i-1),alph(i-2),omeg(i-2),fail,molnum(i-2))
 892               nsi=nsi+1
 893             enddo
 894             if (nsi.gt.maxsi) return 1
 895           endif
 896           call locate_next_res(i-1)
 897         endif
 898         theta(i)=gen_theta(it1,phi(i),phi(i+1),molnum(i))
 899 !        write(iout,*) "theta(i),",theta(i)
 900         if ((it1.ne.10).and.(it1.ne.ntyp1)) then
 901         nsi=0
 902         fail=.true.
 903         do while (fail.and.nsi.le.maxsi)
 904           call gen_side(it1,theta(i),alph(i-1),omeg(i-1),fail,molnum(i))
 905 !                  write(iout,*)"alpha,omeg(i-1)",alph(i-1),omeg(i-1),i,nsi,maxsi
 906           nsi=nsi+1
 907         enddo
 908         if (nsi.gt.maxsi) return 1
 909         endif
 910         call locate_next_res(i)
 911         write(iout,*) "overlap,",overlap(i-1)
 912         if (overlap(i-1)) then
 913           if (nit.lt.maxnit) then
 914             back=.true.
 915             nit=nit+1
 916           else
 917             nit=0
 918             if (i.gt.3) then
 919               back=.true.
 920               i=i-1
 921             else
 922               write (iout,'(a)') &
 923         'Cannot generate non-overlaping conformation. Increase MAXNIT.'
 924               write (*,'(a)') &
 925         'Cannot generate non-overlaping conformation. Increase MAXNIT.'
 926               return 1
 927             endif
 928           endif
 929         else
 930 !          write(iout,*) "tu dochodze"
 931           back=.false.
 932           nit=0
 933           i=i+1
 934         endif
 935         niter=niter+1
 936       enddo
 937       if (niter.ge.maxgen) then
 938         write (iout,'(a,2i5)') &
 939        'Too many trials in conformation generation',niter,maxgen
 940         write (*,'(a,2i5)') &
 941        'Too many trials in conformation generation',niter,maxgen
 942         return 1
 943       endif
 944       do j=1,3
 945         c(j,nres+1)=c(j,1)
 946         c(j,nres+nres)=c(j,nres)
 947       enddo
 948       return
 949       end subroutine gen_rand_conf
 950 !-----------------------------------------------------------------------------
 951       logical function overlap(i)
 952 !      implicit real*8 (a-h,o-z)
 953 !      include 'DIMENSIONS'
 954 !      include 'COMMON.CHAIN'
 955 !      include 'COMMON.INTERACT'
 956 !      include 'COMMON.FFIELD'
 957       integer :: i,j,iti,itj,iteli,itelj,k
 958       real(kind=8) :: redfac,rcomp
 959       integer :: nres2
 960       nres2=2*nres
 961       data redfac /0.5D0/
 962       overlap=.false.
 963       iti=iabs(itype(i,molnum(i)))
 964       if (iti.gt.ntyp) return
 965 ! Check for SC-SC overlaps.
 966 !d    print *,'nnt=',nnt,' nct=',nct
 967       do j=nnt,i-1
 968 !        print *, "molnum(j)",j,molnum(j)
 969         if (molnum(j).eq.1) then
 970         itj=iabs(itype(j,1))
 971         if (itj.eq.ntyp1) cycle
 972         if (j.lt.i-1 .or. ipot.ne.4) then
 973           rcomp=sigmaii(iti,itj)
 974         else
 975           rcomp=sigma(iti,itj)
 976         endif
 977 !d      print *,'j=',j
 978         if (dist(nres+i,nres+j).lt.redfac*rcomp) then
 979           overlap=.true.
 980
 981 !        print *,'overlap, SC-SC: i=',i,' j=',j,
 982 !     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
 983 !     &     rcomp
 984           return
 985         endif
 986         else if (molnum(j).eq.2) then
 987         itj=iabs(itype(j,2))
 988         if (dist(nres+i,nres+j).lt.redfac*sigma_nucl(iti,itj)) then
 989           overlap=.true.
 990
 991 !        print *,'overlap, SC-SC: i=',i,' j=',j,
 992 !     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
 993 !     &     rcomp
 994           return
 995         endif
 996
 997       endif
 998       enddo
 999 ! Check for overlaps between the added peptide group and the preceding
1000 ! SCs.
1001       iteli=itel(i)
1002       do j=1,3
1003 !       c(j,nres2+1)=0.5D0*(c(j,i)+c(j,i+1))
1004         c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1005       enddo
1006       do j=nnt,i-2
1007         if (molnum(j).ne.1) cycle
1008         itj=iabs(itype(j,1))
1009 !d      print *,'overlap, p-Sc: i=',i,' j=',j,
1010 !d   &         ' dist=',dist(nres+j,maxres2+1)
1011         if (dist(nres+j,nres2+3).lt.4.0D0*redfac) then
1012           overlap=.true.
1013           return
1014         endif
1015       enddo
1016 ! Check for overlaps between the added side chain and the preceding peptide
1017 ! groups.
1018       do j=1,nnt-2
1019         if (molnum(j).ne.1) cycle
1020         do k=1,3
1021           c(k,nres2+3)=0.5D0*(c(k,j)+c(k,j+1))
1022         enddo
1023 !d      print *,'overlap, SC-p: i=',i,' j=',j,
1024 !d   &         ' dist=',dist(nres+i,maxres2+1)
1025         if (dist(nres+i,nres2+3).lt.4.0D0*redfac) then
1026           overlap=.true.
1027           return
1028         endif
1029       enddo
1030 ! Check for p-p overlaps
1031       do j=1,3
1032         c(j,nres2+3)=0.5D0*(c(j,i)+c(j,i+1))
1033       enddo
1034       do j=nnt,i-2
1035 !        if (molnum(j).eq.1) then
1036         itelj=itel(j)
1037         do k=1,3
1038           c(k,nres2+4)=0.5D0*(c(k,j)+c(k,j+1))
1039         enddo
1040 !d      print *,'overlap, p-p: i=',i,' j=',j,
1041 !d   &         ' dist=',dist(maxres2+1,maxres2+2)
1042         if (molnum(j).eq.1) then
1043         if(iteli.ne.0.and.itelj.ne.0)then
1044         if (dist(nres2+3,nres2+4).lt.rpp(iteli,itelj)*redfac) then
1045           overlap=.true.
1046           return
1047         endif
1048         endif
1049         else if (molnum(j).eq.2) then
1050         if (dist(nres2+3,nres2+4).lt.3.0) then
1051           overlap=.true.
1052           return
1053         endif
1054       endif
1055       enddo
1056       return
1057       end function overlap
1058 !-----------------------------------------------------------------------------
1059       real(kind=8) function gen_phi(i,it1,it2)
1060       use random, only:ran_number
1061 !      implicit real*8 (a-h,o-z)
1062 !      include 'DIMENSIONS'
1063 !      include 'COMMON.GEO'
1064 !      include 'COMMON.BOUNDS'
1065       integer :: i,it1,it2
1066 !      gen_phi=ran_number(-pi,pi)
1067 ! 8/13/98 Generate phi using pre-defined boundaries
1068       gen_phi=ran_number(phibound(1,i),phibound(2,i))
1069       return
1070       end function gen_phi
1071 !-----------------------------------------------------------------------------
1072       real(kind=8) function gen_theta(it,gama,gama1,mnum)
1073       use random,only:binorm,ran_number
1074 !      implicit real*8 (a-h,o-z)
1075 !      include 'DIMENSIONS'
1076 !      include 'COMMON.LOCAL'
1077 !      include 'COMMON.GEO'
1078       real(kind=8),dimension(2) :: y,z
1079       real(kind=8) :: theta_max,theta_min,sig,ak
1080 !el local variables
1081       integer :: j,it,k,mnum
1082       real(kind=8) :: gama,gama1,thet_pred_mean,theta_temp
1083 !     print *,'gen_theta: it=',it
1084       theta_min=0.05D0*pi
1085       theta_max=0.95D0*pi
1086       if (dabs(gama).gt.dwapi) then
1087         y(1)=dcos(gama)
1088         y(2)=dsin(gama)
1089       else
1090         y(1)=0.0D0
1091         y(2)=0.0D0
1092       endif
1093       if (dabs(gama1).gt.dwapi) then
1094         z(1)=dcos(gama1)
1095         z(2)=dsin(gama1)
1096       else
1097         z(1)=0.0D0
1098         z(2)=0.0D0
1099       endif
1100       if (it.eq.ntyp1) then
1101       gen_theta=ran_number(theta_max/2.0,theta_max)
1102       else if (mnum.eq.1) then
1103
1104       thet_pred_mean=a0thet(it)
1105 !      write(iout,*),it,thet_pred_mean,"gen_thet"
1106       do k=1,2
1107         thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1108            +bthet(k,it,1,1)*z(k)
1109       enddo
1110       sig=polthet(3,it)
1111       do j=2,0,-1
1112         sig=sig*thet_pred_mean+polthet(j,it)
1113       enddo
1114       sig=0.5D0/(sig*sig+sigc0(it))
1115       ak=dexp(gthet(1,it)- &
1116        0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1117 !     print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1118 !     print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1119       theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1120       if (theta_temp.lt.theta_min) theta_temp=theta_min
1121       if (theta_temp.gt.theta_max) theta_temp=theta_max
1122       gen_theta=theta_temp
1123 !     print '(a)','Exiting GENTHETA.'
1124       else if (mnum.eq.2) then
1125        gen_theta=2.0d0 + ran_number(0.0d0,0.34d0)
1126       else
1127               gen_theta=ran_number(theta_max/2.0,theta_max)
1128        endif
1129       return
1130       end function gen_theta
1131 !-----------------------------------------------------------------------------
1132       subroutine gen_side(it,the,al,om,fail,mnum)
1133       use random, only:ran_number,mult_norm1
1134 !      implicit real*8 (a-h,o-z)
1135 !      include 'DIMENSIONS'
1136 !      include 'COMMON.GEO'
1137 !      include 'COMMON.LOCAL'
1138 !      include 'COMMON.SETUP'
1139 !      include 'COMMON.IOUNITS'
1140       real(kind=8) :: MaxBoxLen=10.0D0
1141       real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1142       real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1143       real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1144       real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1145       real(kind=8),dimension(2) :: y,cm,eig
1146       real(kind=8),dimension(2,2) :: box
1147       real(kind=8),dimension(100) :: work
1148       real(kind=8) :: eig_limit=1.0D-8
1149       real(kind=8) :: Big=10.0D0
1150       logical :: lprint,fail,lcheck
1151 !el local variables
1152       integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob,mnum
1153       real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1154       real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1155       real(kind=8) :: which_lobe
1156       lcheck=.false.
1157       lprint=.false.
1158       fail=.false.
1159       if (mnum.eq.1) then
1160       if (the.eq.0.0D0 .or. the.eq.pi) then
1161 #ifdef MPI
1162         write (*,'(a,i4,a,i3,a,1pe14.5)') &
1163        'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1164 #else
1165 !d        write (iout,'(a,i3,a,1pe14.5)')
1166 !d     &   'Error in GenSide: it=',it,' theta=',the
1167 #endif
1168         fail=.true.
1169         return
1170       endif
1171       if (nlobit.eq.0) then
1172          al=ran_number(0.05d0,pi/2)
1173          om=ran_number(-pi,pi)
1174          return
1175       endif
1176       tant=dtan(the-pipol)
1177       nlobit=nlob(it)
1178       allocate(z(3,nlobit))
1179       allocate(W1(nlobit))
1180       allocate(detAp(nlobit))
1181       allocate(sumW(0:nlobit))
1182       if (lprint) then
1183 #ifdef MPI
1184         print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1185         write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1186 #endif
1187         print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1188         write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1189            ' tant=',tant
1190       endif
1191       do i=1,nlobit
1192        zz1=tant-censc(1,i,it)
1193         do k=1,3
1194           do l=1,3
1195             a(k,l)=gaussc(k,l,i,it)
1196           enddo
1197         enddo
1198         detApi=a(2,2)*a(3,3)-a(2,3)**2
1199         Ap_inv(2,2)=a(3,3)/detApi
1200         Ap_inv(2,3)=-a(2,3)/detApi
1201         Ap_inv(3,2)=Ap_inv(2,3)
1202         Ap_inv(3,3)=a(2,2)/detApi
1203         if (lprint) then
1204           write (*,'(/a,i2/)') 'Cluster #',i
1205           write (*,'(3(1pe14.5),5x,1pe14.5)') &
1206           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1207           write (iout,'(/a,i2/)') 'Cluster #',i
1208           write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1209           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1210         endif
1211         W1i=0.0D0
1212         do k=2,3
1213           do l=2,3
1214             W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1215           enddo
1216         enddo
1217         W1i=a(1,1)-W1i
1218         W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1219 !        if (lprint) write(*,'(a,3(1pe15.5)/)')
1220 !     &          'detAp, W1, anormi',detApi,W1i,anormi
1221         do k=2,3
1222           zk=censc(k,i,it)
1223           do l=2,3
1224             zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1225           enddo
1226           z(k,i)=zk
1227         enddo
1228         detAp(i)=dsqrt(detApi)
1229       enddo
1230
1231       if (lprint) then
1232         print *,'W1:',(w1(i),i=1,nlobit)
1233         print *,'detAp:',(detAp(i),i=1,nlobit)
1234         print *,'Z'
1235         do i=1,nlobit
1236           print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1237         enddo
1238         write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1239         write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1240         write (iout,*) 'Z'
1241         do i=1,nlobit
1242           write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1243         enddo
1244       endif
1245       if (lcheck) then
1246 ! Writing the distribution just to check the procedure
1247       fac=0.0D0
1248       dV=deg2rad**2*10.0D0
1249       sum=0.0D0
1250       sum1=0.0D0
1251       do i=1,nlobit
1252         fac=fac+W1(i)/detAp(i)
1253       enddo
1254       fac=1.0D0/(2.0D0*fac*pi)
1255 !d    print *,it,'fac=',fac
1256       do ial=90,180,2
1257         y(1)=deg2rad*ial
1258         do iom=-180,180,5
1259           y(2)=deg2rad*iom
1260           wart=0.0D0
1261           do i=1,nlobit
1262             do j=2,3
1263               do k=2,3
1264                 a(j-1,k-1)=gaussc(j,k,i,it)
1265               enddo
1266             enddo
1267             y2=y(2)
1268
1269             do iii=-1,1
1270
1271               y(2)=y2+iii*dwapi
1272
1273               wykl=0.0D0
1274               do j=1,2
1275                 do k=1,2
1276                   wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1277                 enddo
1278               enddo
1279               wart=wart+W1(i)*dexp(-0.5D0*wykl)
1280
1281             enddo
1282
1283             y(2)=y2
1284
1285           enddo
1286 !         print *,'y',y(1),y(2),' fac=',fac
1287           wart=fac*wart
1288           write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1289           sum=sum+wart
1290           sum1=sum1+1.0D0
1291         enddo
1292       enddo
1293 !     print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1294       return
1295       endif
1296
1297 ! Calculate the CM of the system
1298 !
1299       do i=1,nlobit
1300         W1(i)=W1(i)/detAp(i)
1301       enddo
1302       sumW(0)=0.0D0
1303       do i=1,nlobit
1304         sumW(i)=sumW(i-1)+W1(i)
1305       enddo
1306       cm(1)=z(2,1)*W1(1)
1307       cm(2)=z(3,1)*W1(1)
1308       do j=2,nlobit
1309         cm(1)=cm(1)+z(2,j)*W1(j)
1310         cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1311       enddo
1312       cm(1)=cm(1)/sumW(nlobit)
1313       cm(2)=cm(2)/sumW(nlobit)
1314       if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1315        cm(2).gt.Big .or. cm(2).lt.-Big) then
1316 !d        write (iout,'(a)')
1317 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1318 !d        write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1319 !d        write (*,'(a)')
1320 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1321 !d        write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1322         fail=.true.
1323         return
1324       endif
1325 !d    print *,'CM:',cm(1),cm(2)
1326 !
1327 ! Find the largest search distance from CM
1328 !
1329       radmax=0.0D0
1330       do i=1,nlobit
1331         do j=2,3
1332           do k=2,3
1333             a(j-1,k-1)=gaussc(j,k,i,it)
1334           enddo
1335         enddo
1336 #ifdef NAG
1337         call f02faf('N','U',2,a,3,eig,work,100,ifail)
1338 #else
1339         call djacob(2,3,10000,1.0d-10,a,vec,eig)
1340 #endif
1341 #ifdef MPI
1342         if (lprint) then
1343           print *,'*************** CG Processor',me
1344           print *,'CM:',cm(1),cm(2)
1345           write (iout,*) '*************** CG Processor',me
1346           write (iout,*) 'CM:',cm(1),cm(2)
1347           print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1348           write (iout,'(A,8f10.5)') &
1349               'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1350         endif
1351 #endif
1352         if (eig(1).lt.eig_limit) then
1353           write(iout,'(a)') &
1354            'From Mult_Norm: Eigenvalues of A are too small.'
1355           write(*,'(a)') &
1356            'From Mult_Norm: Eigenvalues of A are too small.'
1357           fail=.true.
1358           return
1359         endif
1360         radius=0.0D0
1361 !d      print *,'i=',i
1362         do j=1,2
1363           radius=radius+pinorm(z(j+1,i)-cm(j))**2
1364         enddo
1365         radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1366         if (radius.gt.radmax) radmax=radius
1367       enddo
1368       if (radmax.gt.pi) radmax=pi
1369 !
1370 ! Determine the boundaries of the search rectangle.
1371 !
1372       if (lprint) then
1373         print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1374         print '(a,4(1pe14.4))','radmax: ',radmax
1375       endif
1376       box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1377       box(2,1)=dmin1(cm(1)+radmax,pi)
1378       box(1,2)=cm(2)-radmax
1379       box(2,2)=cm(2)+radmax
1380       if (lprint) then
1381 #ifdef MPI
1382         print *,'CG Processor',me,' Array BOX:'
1383 #else
1384         print *,'Array BOX:'
1385 #endif
1386         print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1387         print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1388 #ifdef MPI
1389         write (iout,*)'CG Processor',me,' Array BOX:'
1390 #else
1391         write (iout,*)'Array BOX:'
1392 #endif
1393         write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1394         write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1395       endif
1396 !      if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1397 !#ifdef MPI
1398 !        write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1399 !        write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1400 !#else
1401 !        write (iout,'(a)') 'Bad sampling box.'
1402 !#endif
1403 !        fail=.true.
1404 !        return
1405 !      endif
1406       which_lobe=ran_number(0.0D0,sumW(nlobit))
1407 !     print '(a,1pe14.4)','which_lobe=',which_lobe
1408       do i=1,nlobit
1409         if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1410       enddo
1411     1 ilob=i
1412 !     print *,'ilob=',ilob,' nlob=',nlob(it)
1413       do i=2,3
1414         cm(i-1)=z(i,ilob)
1415         do j=2,3
1416           a(i-1,j-1)=gaussc(i,j,ilob,it)
1417         enddo
1418       enddo
1419 !d    print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1420       call mult_norm1(3,2,a,cm,box,y,fail)
1421       if (fail) return
1422       al=y(1)
1423       om=pinorm(y(2))
1424       else if (mnum.eq.2) then
1425        al=0.7+ran_number(0.0d0,0.2d0)
1426        om=ran_number(0.0d0,3.14d0)
1427       endif
1428
1429 !d    print *,'al=',al,' om=',om
1430 !d    stop
1431       return
1432       end subroutine gen_side
1433 !-----------------------------------------------------------------------------
1434       subroutine overlap_sc(scfail)
1435 !
1436 !     Internal and cartesian coordinates must be consistent as input,
1437 !     and will be up-to-date on return.
1438 !     At the end of this procedure, scfail is true if there are
1439 !     overlapping residues left, or false otherwise (success)
1440 !
1441 !      implicit real*8 (a-h,o-z)
1442 !      include 'DIMENSIONS'
1443 !      include 'COMMON.CHAIN'
1444 !      include 'COMMON.INTERACT'
1445 !      include 'COMMON.FFIELD'
1446 !      include 'COMMON.VAR'
1447 !      include 'COMMON.SBRIDGE'
1448 !      include 'COMMON.IOUNITS'
1449       logical :: had_overlaps,fail,scfail
1450       integer,dimension(nres) :: ioverlap !(maxres)
1451       integer :: ioverlap_last,k,maxsi,i,iti,nsi
1452       integer :: ires,j
1453
1454       had_overlaps=.false.
1455       call overlap_sc_list(ioverlap,ioverlap_last)
1456       if (ioverlap_last.gt.0) then
1457         write (iout,*) '#OVERLAPing residues ',ioverlap_last
1458         write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1459         had_overlaps=.true.
1460       endif
1461
1462       maxsi=1000
1463       do k=1,1000
1464         if (ioverlap_last.eq.0) exit
1465
1466         do ires=1,ioverlap_last
1467           i=ioverlap(ires)
1468           iti=iabs(itype(i,1))
1469           if ((iti.ne.10).and.(molnum(i).ne.5).and.(iti.ne.ntyp1)) then
1470             nsi=0
1471             fail=.true.
1472             do while (fail.and.nsi.le.maxsi)
1473               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1474               nsi=nsi+1
1475             enddo
1476             if(fail) goto 999
1477           endif
1478         enddo
1479
1480         call chainbuild
1481         call overlap_sc_list(ioverlap,ioverlap_last)
1482 !        write (iout,*) 'Overlaping residues ',ioverlap_last,
1483 !     &           (ioverlap(j),j=1,ioverlap_last)
1484       enddo
1485
1486       if (k.le.1000.and.ioverlap_last.eq.0) then
1487         scfail=.false.
1488         if (had_overlaps) then
1489           write (iout,*) '#OVERLAPing all corrected after ',k,&
1490                ' random generation'
1491         endif
1492       else
1493         scfail=.true.
1494         write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1495         write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1496       endif
1497
1498       return
1499
1500  999  continue
1501       write (iout,'(a30,i5,a12,i4)') &
1502                      '#OVERLAP FAIL in gen_side after',maxsi,&
1503                      'iter for RES',i
1504       scfail=.true.
1505       return
1506       end subroutine overlap_sc
1507 !-----------------------------------------------------------------------------
1508       subroutine overlap_sc_list(ioverlap,ioverlap_last)
1509       use calc_data
1510 !      implicit real*8 (a-h,o-z)
1511 !      include 'DIMENSIONS'
1512 !      include 'COMMON.GEO'
1513 !      include 'COMMON.LOCAL'
1514 !      include 'COMMON.IOUNITS'
1515 !      include 'COMMON.CHAIN'
1516 !      include 'COMMON.INTERACT'
1517 !      include 'COMMON.FFIELD'
1518 !      include 'COMMON.VAR'
1519 !      include 'COMMON.CALC'
1520       logical :: fail
1521       integer,dimension(nres) :: ioverlap !(maxres)
1522       integer :: ioverlap_last
1523 !el local variables
1524       integer :: ind,iint
1525       real(kind=8) :: redfac,sig        !rrij,sigsq,
1526       integer :: itypi,itypj,itypi1
1527       real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1528       data redfac /0.5D0/
1529
1530       ioverlap_last=0
1531 ! Check for SC-SC overlaps and mark residues
1532 !      print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1533       ind=0
1534       do i=iatsc_s,iatsc_e
1535         if (itype(i,molnum(i)).eq.ntyp1_molec(molnum(i))) cycle
1536         if (molnum(i).eq.5) print *,"WTF",i,iatsc_s,iatsc_e
1537         if (molnum(i).eq.5) cycle
1538         itypi=iabs(itype(i,molnum(i)))
1539         itypi1=iabs(itype(i+1,1))
1540         xi=c(1,nres+i)
1541         yi=c(2,nres+i)
1542         zi=c(3,nres+i)
1543         dxi=dc_norm(1,nres+i)
1544         dyi=dc_norm(2,nres+i)
1545         dzi=dc_norm(3,nres+i)
1546         dsci_inv=dsc_inv(itypi)
1547 !
1548        do iint=1,nint_gr(i)
1549          do j=istart(i,iint),iend(i,iint)
1550          if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
1551             ind=ind+1
1552             itypj=iabs(itype(j,molnum(j)))
1553             dscj_inv=dsc_inv(itypj)
1554             sig0ij=sigma(itypi,itypj)
1555             chi1=chi(itypi,itypj)
1556             chi2=chi(itypj,itypi)
1557             chi12=chi1*chi2
1558             chip1=chip(itypi)
1559             chip2=chip(itypj)
1560             chip12=chip1*chip2
1561             alf1=alp(itypi)
1562             alf2=alp(itypj)
1563             alf12=0.5D0*(alf1+alf2)
1564           if (j.gt.i+1) then
1565            rcomp=sigmaii(itypi,itypj)
1566           else
1567            rcomp=sigma(itypi,itypj)
1568           endif
1569 !         print '(2(a3,2i3),a3,2f10.5)',
1570 !     &        ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1571 !     &        ,rcomp
1572             xj=c(1,nres+j)-xi
1573             yj=c(2,nres+j)-yi
1574             zj=c(3,nres+j)-zi
1575             dxj=dc_norm(1,nres+j)
1576             dyj=dc_norm(2,nres+j)
1577             dzj=dc_norm(3,nres+j)
1578             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1579             rij=dsqrt(rrij)
1580             call sc_angular
1581             sigsq=1.0D0/sigsq
1582             sig=sig0ij*dsqrt(sigsq)
1583             rij_shift=1.0D0/rij-sig+sig0ij
1584
1585 !t          if ( 1.0/rij .lt. redfac*rcomp .or.
1586 !t     &       rij_shift.le.0.0D0 ) then
1587             if ( rij_shift.le.0.0D0 ) then
1588 !d           write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1589 !d     &     'overlap SC-SC: i=',i,' j=',j,
1590 !d     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
1591 !d     &     rcomp,1.0/rij,rij_shift
1592           ioverlap_last=ioverlap_last+1
1593           ioverlap(ioverlap_last)=i
1594           do k=1,ioverlap_last-1
1595            if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1596           enddo
1597           ioverlap_last=ioverlap_last+1
1598           ioverlap(ioverlap_last)=j
1599           do k=1,ioverlap_last-1
1600            if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1601           enddo
1602          endif
1603         enddo
1604        enddo
1605       enddo
1606       return
1607       end subroutine overlap_sc_list
1608 #endif
1609 !-----------------------------------------------------------------------------
1610 ! energy_p_new_barrier.F
1611 !-----------------------------------------------------------------------------
1612       subroutine sc_angular
1613 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1614 ! om12. Called by ebp, egb, and egbv.
1615       use calc_data
1616 !      implicit none
1617 !      include 'COMMON.CALC'
1618 !      include 'COMMON.IOUNITS'
1619       erij(1)=xj*rij
1620       erij(2)=yj*rij
1621       erij(3)=zj*rij
1622       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1623       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1624       om12=dxi*dxj+dyi*dyj+dzi*dzj
1625       chiom12=chi12*om12
1626 ! Calculate eps1(om12) and its derivative in om12
1627       faceps1=1.0D0-om12*chiom12
1628       faceps1_inv=1.0D0/faceps1
1629       eps1=dsqrt(faceps1_inv)
1630 ! Following variable is eps1*deps1/dom12
1631       eps1_om12=faceps1_inv*chiom12
1632 ! diagnostics only
1633 !      faceps1_inv=om12
1634 !      eps1=om12
1635 !      eps1_om12=1.0d0
1636 !      write (iout,*) "om12",om12," eps1",eps1
1637 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1638 ! and om12.
1639       om1om2=om1*om2
1640       chiom1=chi1*om1
1641       chiom2=chi2*om2
1642       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1643       sigsq=1.0D0-facsig*faceps1_inv
1644       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1645       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1646       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1647 ! diagnostics only
1648 !      sigsq=1.0d0
1649 !      sigsq_om1=0.0d0
1650 !      sigsq_om2=0.0d0
1651 !      sigsq_om12=0.0d0
1652 !      write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1653 !      write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1654 !     &    " eps1",eps1
1655 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1656       chipom1=chip1*om1
1657       chipom2=chip2*om2
1658       chipom12=chip12*om12
1659       facp=1.0D0-om12*chipom12
1660       facp_inv=1.0D0/facp
1661       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1662 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1663 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1664 ! Following variable is the square root of eps2
1665       eps2rt=1.0D0-facp1*facp_inv
1666 ! Following three variables are the derivatives of the square root of eps
1667 ! in om1, om2, and om12.
1668       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1669       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1670       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1671 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1672       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1673 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1674 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1675 !     &  " eps2rt_om12",eps2rt_om12
1676 ! Calculate whole angle-dependent part of epsilon and contributions
1677 ! to its derivatives
1678       return
1679       end subroutine sc_angular
1680 !-----------------------------------------------------------------------------
1681 ! initialize_p.F
1682       subroutine sc_angular_nucl
1683 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1684 ! om12. Called by ebp, egb, and egbv.
1685 !      use calc_data
1686 !      implicit none
1687 !      include 'COMMON.CALC'
1688 !      include 'COMMON.IOUNITS'
1689       use comm_locel
1690       use calc_data_nucl
1691       erij(1)=xj*rij
1692       erij(2)=yj*rij
1693       erij(3)=zj*rij
1694       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1695       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1696       om12=dxi*dxj+dyi*dyj+dzi*dzj
1697       chiom12=chi12*om12
1698 ! Calculate eps1(om12) and its derivative in om12
1699       faceps1=1.0D0-om12*chiom12
1700       faceps1_inv=1.0D0/faceps1
1701       eps1=dsqrt(faceps1_inv)
1702 ! Following variable is eps1*deps1/dom12
1703       eps1_om12=faceps1_inv*chiom12
1704 ! diagnostics only
1705 !      faceps1_inv=om12
1706 !      eps1=om12
1707 !      eps1_om12=1.0d0
1708 !      write (iout,*) "om12",om12," eps1",eps1
1709 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1710 ! and om12.
1711       om1om2=om1*om2
1712       chiom1=chi1*om1
1713       chiom2=chi2*om2
1714       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1715       sigsq=1.0D0-facsig*faceps1_inv
1716       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1717       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1718       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1719       chipom1=chip1*om1
1720       chipom2=chip2*om2
1721       chipom12=chip12*om12
1722       facp=1.0D0-om12*chipom12
1723       facp_inv=1.0D0/facp
1724       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1725 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1726 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1727 ! Following variable is the square root of eps2
1728       eps2rt=1.0D0-facp1*facp_inv
1729 ! Following three variables are the derivatives of the square root of eps
1730 ! in om1, om2, and om12.
1731       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1732       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1733       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1734 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1735       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1736 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1737 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1738 !     &  " eps2rt_om12",eps2rt_om12
1739 ! Calculate whole angle-dependent part of epsilon and contributions
1740 ! to its derivatives
1741       return
1742       end subroutine sc_angular_nucl
1743
1744 !-----------------------------------------------------------------------------
1745       subroutine int_bounds(total_ints,lower_bound,upper_bound)
1746 !      implicit real*8 (a-h,o-z)
1747 !      include 'DIMENSIONS'
1748       include 'mpif.h'
1749 !      include 'COMMON.SETUP'
1750       integer :: total_ints,lower_bound,upper_bound,nint
1751       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1752       integer :: i,nexcess
1753       nint=total_ints/nfgtasks
1754       do i=1,nfgtasks
1755         int4proc(i-1)=nint
1756       enddo
1757       nexcess=total_ints-nint*nfgtasks
1758       do i=1,nexcess
1759         int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1760       enddo
1761       lower_bound=0
1762       do i=0,fg_rank-1
1763         lower_bound=lower_bound+int4proc(i)
1764       enddo
1765       upper_bound=lower_bound+int4proc(fg_rank)
1766       lower_bound=lower_bound+1
1767       return
1768       end subroutine int_bounds
1769 !-----------------------------------------------------------------------------
1770       subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1771 !      implicit real*8 (a-h,o-z)
1772 !      include 'DIMENSIONS'
1773       include 'mpif.h'
1774 !      include 'COMMON.SETUP'
1775       integer :: total_ints,lower_bound,upper_bound,nint
1776       integer :: nexcess,i
1777       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1778       nint=total_ints/nfgtasks1
1779       do i=1,nfgtasks1
1780         int4proc(i-1)=nint
1781       enddo
1782       nexcess=total_ints-nint*nfgtasks1
1783       do i=1,nexcess
1784         int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1785       enddo
1786       lower_bound=0
1787       do i=0,fg_rank1-1
1788         lower_bound=lower_bound+int4proc(i)
1789       enddo
1790       upper_bound=lower_bound+int4proc(fg_rank1)
1791       lower_bound=lower_bound+1
1792       return
1793       end subroutine int_bounds1
1794 !-----------------------------------------------------------------------------
1795 ! intcartderiv.F
1796 !-----------------------------------------------------------------------------
1797       subroutine chainbuild_cart
1798 !      implicit real*8 (a-h,o-z)
1799 !      include 'DIMENSIONS'
1800       use control_data
1801 #ifdef MPI
1802       include 'mpif.h'
1803 #endif
1804 !      include 'COMMON.SETUP'
1805 !      include 'COMMON.CHAIN'
1806 !      include 'COMMON.LOCAL'
1807 !      include 'COMMON.TIME1'
1808 !      include 'COMMON.IOUNITS'
1809       integer :: j,i,ierror,ierr
1810       real(kind=8) :: time00,time01
1811 #ifdef MPI
1812       if (nfgtasks.gt.1) then
1813 !        write (iout,*) "BCAST in chainbuild_cart"
1814 !        call flush(iout)
1815 ! Broadcast the order to build the chain and compute internal coordinates
1816 ! to the slaves. The slaves receive the order in ERGASTULUM.
1817         time00=MPI_Wtime()
1818 !      write (iout,*) "CHAINBUILD_CART: DC before BCAST"
1819 !      do i=0,nres
1820 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1821 !     &   (dc(j,i+nres),j=1,3)
1822 !      enddo
1823         if (fg_rank.eq.0) &
1824           call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1825         time_bcast7=time_bcast7+MPI_Wtime()-time00
1826         time01=MPI_Wtime()
1827         call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1828           king,FG_COMM,IERR)
1829 !      write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1830 !      do i=0,nres
1831 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1832 !     &   (dc(j,i+nres),j=1,3)
1833 !      enddo
1834 !        write (iout,*) "End BCAST in chainbuild_cart"
1835 !        call flush(iout)
1836         time_bcast=time_bcast+MPI_Wtime()-time00
1837         time_bcastc=time_bcastc+MPI_Wtime()-time01
1838       endif
1839 #endif
1840       do j=1,3
1841         c(j,1)=dc(j,0)
1842       enddo
1843       do i=2,nres
1844         do j=1,3
1845           c(j,i)=c(j,i-1)+dc(j,i-1)
1846         enddo
1847       enddo
1848       do i=1,nres
1849         do j=1,3
1850           c(j,i+nres)=c(j,i)+dc(j,i+nres)
1851         enddo
1852       enddo
1853 !      write (iout,*) "CHAINBUILD_CART"
1854 !      call cartprint
1855       call int_from_cart1(.false.)
1856       return
1857       end subroutine chainbuild_cart
1858 !-----------------------------------------------------------------------------
1859 ! intcor.f
1860 !-----------------------------------------------------------------------------
1861       real(kind=8) function alpha(i1,i2,i3)
1862 !
1863 !  Calculates the planar angle between atoms (i1), (i2), and (i3).
1864 !
1865 !      implicit real*8 (a-h,o-z)
1866 !      include 'DIMENSIONS'
1867 !      include 'COMMON.GEO'
1868 !      include 'COMMON.CHAIN'
1869 !el local variables
1870       integer :: i1,i2,i3
1871       real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1872       x12=c(1,i1)-c(1,i2)
1873       x23=c(1,i3)-c(1,i2)
1874       y12=c(2,i1)-c(2,i2)
1875       y23=c(2,i3)-c(2,i2)
1876       z12=c(3,i1)-c(3,i2)
1877       z23=c(3,i3)-c(3,i2)
1878       vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1879       wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1880       scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1881       alpha=arcos(scalar)
1882       return
1883       end function alpha
1884 !-----------------------------------------------------------------------------
1885       real(kind=8) function beta(i1,i2,i3,i4)
1886 !
1887 !  Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1888 !
1889 !      implicit real*8 (a-h,o-z)
1890 !      include 'DIMENSIONS'
1891 !      include 'COMMON.GEO'
1892 !      include 'COMMON.CHAIN'
1893 !el local variables
1894       integer :: i1,i2,i3,i4
1895       real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1896       real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1897       real(kind=8) :: tx,ty,tz
1898       x12=c(1,i1)-c(1,i2)
1899       x23=c(1,i3)-c(1,i2)
1900       x34=c(1,i4)-c(1,i3)
1901       y12=c(2,i1)-c(2,i2)
1902       y23=c(2,i3)-c(2,i2)
1903       y34=c(2,i4)-c(2,i3)
1904       z12=c(3,i1)-c(3,i2)
1905       z23=c(3,i3)-c(3,i2)
1906       z34=c(3,i4)-c(3,i3)
1907 !d    print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1908 !d    print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1909 !d    print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1910       wx=-y23*z34+y34*z23
1911       wy=x23*z34-z23*x34
1912       wz=-x23*y34+y23*x34
1913       wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1914       vx=y12*z23-z12*y23
1915       vy=-x12*z23+z12*x23
1916       vz=x12*y23-y12*x23
1917       vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1918       if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1919       scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1920       if (dabs(scalar).gt.1.0D0) &
1921       scalar=0.99999999999999D0*scalar/dabs(scalar)
1922       angle=dacos(scalar)
1923 !d    print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1924 !d   &scalar,angle
1925       else
1926       angle=pi
1927       endif
1928 !     if (angle.le.0.0D0) angle=pi+angle
1929       tx=vy*wz-vz*wy
1930       ty=-vx*wz+vz*wx
1931       tz=vx*wy-vy*wx
1932       scalar=tx*x23+ty*y23+tz*z23
1933       if (scalar.lt.0.0D0) angle=-angle
1934       beta=angle
1935       return
1936       end function beta
1937 !-----------------------------------------------------------------------------
1938       real(kind=8) function dist(i1,i2)
1939 !
1940 !  Calculates the distance between atoms (i1) and (i2).
1941 !
1942 !      implicit real*8 (a-h,o-z)
1943 !      include 'DIMENSIONS'
1944 !      include 'COMMON.GEO'
1945 !      include 'COMMON.CHAIN'
1946 !el local variables
1947       integer :: i1,i2
1948       real(kind=8) :: x12,y12,z12
1949       x12=c(1,i1)-c(1,i2)
1950       y12=c(2,i1)-c(2,i2)
1951       z12=c(3,i1)-c(3,i2)
1952       dist=dsqrt(x12*x12+y12*y12+z12*z12)
1953       return
1954       end function dist
1955 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1956 !-----------------------------------------------------------------------------
1957 ! local_move.f
1958 !-----------------------------------------------------------------------------
1959       subroutine local_move_init(debug)
1960 !rc      implicit none
1961
1962 !     Includes
1963 !      implicit real*8 (a-h,o-z)
1964 !      include 'DIMENSIONS'  ! Needed by COMMON.LOCAL
1965 !      include 'COMMON.GEO'  ! For pi, deg2rad
1966 !      include 'COMMON.LOCAL'  ! For vbl
1967 !      include 'COMMON.LOCMOVE'
1968
1969 !     INPUT arguments
1970       logical :: debug
1971
1972
1973 !     Determine wheter to do some debugging output
1974       locmove_output=debug
1975
1976 !     Set the init_called flag to 1
1977       init_called=1
1978
1979 !     The following are never changed
1980       min_theta=60.D0*deg2rad  ! (0,PI)
1981       max_theta=175.D0*deg2rad  ! (0,PI)
1982       dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1983       dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1984       flag=1.0D300
1985       small=1.0D-5
1986       small2=0.5*small*small
1987
1988 !     Not really necessary...
1989       a_n=0
1990       b_n=0
1991       res_n=0
1992
1993       return
1994       end subroutine local_move_init
1995 !-----------------------------------------------------------------------------
1996       subroutine local_move(n_start, n_end, PHImin, PHImax)
1997 !     Perform a local move between residues m and n (inclusive)
1998 !     PHImin and PHImax [0,PI] determine the size of the move
1999 !     Works on whatever structure is in the variables theta and phi,
2000 !     sidechain variables are left untouched
2001 !     The final structure is NOT minimized, but both the cartesian
2002 !     variables c and the angles are up-to-date at the end (no further
2003 !     chainbuild is required)
2004 !rc      implicit none
2005       use random,only:ran_number
2006 !     Includes
2007 !      implicit real*8 (a-h,o-z)
2008 !      include 'DIMENSIONS'
2009 !      include 'COMMON.GEO'
2010 !      include 'COMMON.CHAIN'
2011 !      include 'COMMON.VAR'
2012 !      include 'COMMON.MINIM'
2013 !      include 'COMMON.SBRIDGE'
2014 !      include 'COMMON.LOCMOVE'
2015
2016 !     External functions
2017 !EL      integer move_res
2018 !EL      external move_res
2019 !EL      double precision ran_number
2020 !EL      external ran_number
2021
2022 !     INPUT arguments
2023       integer :: n_start, n_end  ! First and last residues to move
2024       real(kind=8) :: PHImin, PHImax  ! min/max angles [0,PI]
2025
2026 !     Local variables
2027       integer :: i,j
2028       real(kind=8) :: min,max
2029       integer :: iretcode
2030
2031
2032 !     Check if local_move_init was called.  This assumes that it
2033 !     would not be 1 if not explicitely initialized
2034       if (init_called.ne.1) then
2035         write(6,*)'   ***   local_move_init not called!!!'
2036         stop
2037       endif
2038
2039 !     Quick check for crazy range
2040       if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2041         write(6,'(a,i3,a,i3)') &
2042              '   ***   Cannot make local move between n_start = ',&
2043              n_start,' and n_end = ',n_end
2044         return
2045       endif
2046
2047 !     Take care of end residues first...
2048       if (n_start.eq.1) then
2049 !     Move residue 1 (completely random)
2050         theta(3)=ran_number(min_theta,max_theta)
2051         phi(4)=ran_number(-PI,PI)
2052         i=2
2053       else
2054         i=n_start
2055       endif
2056       if (n_end.eq.nres) then
2057 !     Move residue nres (completely random)
2058         theta(nres)=ran_number(min_theta,max_theta)
2059         phi(nres)=ran_number(-PI,PI)
2060         j=nres-1
2061       else
2062         j=n_end
2063       endif
2064
2065 !     ...then go through all other residues one by one
2066 !     Start from the two extremes and converge
2067       call chainbuild
2068       do while (i.le.j)
2069         min=PHImin
2070         max=PHImax
2071 !$$$c     Move the first two residues by less than the others
2072 !$$$        if (i-n_start.lt.3) then
2073 !$$$          if (i-n_start.eq.0) then
2074 !$$$            min=0.4*PHImin
2075 !$$$            max=0.4*PHImax
2076 !$$$          else if (i-n_start.eq.1) then
2077 !$$$            min=0.8*PHImin
2078 !$$$            max=0.8*PHImax
2079 !$$$          else if (i-n_start.eq.2) then
2080 !$$$            min=PHImin
2081 !$$$            max=PHImax
2082 !$$$          endif
2083 !$$$        endif
2084
2085 !     The actual move, on residue i
2086         iretcode=move_res(min,max,i)  ! Discard iretcode
2087         i=i+1
2088
2089         if (i.le.j) then
2090           min=PHImin
2091           max=PHImax
2092 !$$$c     Move the last two residues by less than the others
2093 !$$$          if (n_end-j.lt.3) then
2094 !$$$            if (n_end-j.eq.0) then
2095 !$$$              min=0.4*PHImin
2096 !$$$              max=0.4*PHImax
2097 !$$$            else if (n_end-j.eq.1) then
2098 !$$$              min=0.8*PHImin
2099 !$$$              max=0.8*PHImax
2100 !$$$            else if (n_end-j.eq.2) then
2101 !$$$              min=PHImin
2102 !$$$              max=PHImax
2103 !$$$            endif
2104 !$$$          endif
2105
2106 !     The actual move, on residue j
2107           iretcode=move_res(min,max,j)  ! Discard iretcode
2108           j=j-1
2109         endif
2110       enddo
2111
2112       call int_from_cart(.false.,.false.)
2113
2114       return
2115       end subroutine local_move
2116 !-----------------------------------------------------------------------------
2117       subroutine output_tabs
2118 !     Prints out the contents of a_..., b_..., res_...
2119 !      implicit none
2120
2121 !     Includes
2122 !      include 'COMMON.GEO'
2123 !      include 'COMMON.LOCMOVE'
2124
2125 !     Local variables
2126       integer :: i,j
2127
2128       write(6,*)'a_...'
2129       write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2130       write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2131
2132       write(6,*)'b_...'
2133       write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2134       write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2135
2136       write(6,*)'res_...'
2137       write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2138       write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2139       write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2140       write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2141
2142       return
2143       end subroutine output_tabs
2144 !-----------------------------------------------------------------------------
2145       subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2146 !     Only uses angles if [0,PI] (but PHImin cannot be 0.,
2147 !     and PHImax cannot be PI)
2148 !      implicit none
2149
2150 !     Includes
2151 !      include 'COMMON.GEO'
2152
2153 !     INPUT arguments
2154       real(kind=8) :: PHImin,PHImax
2155
2156 !     OUTPUT arguments
2157       integer :: n
2158       real(kind=8),dimension(0:3) :: ang
2159       logical,dimension(0:2,0:3) :: tab
2160
2161
2162       if (PHImin .eq. PHImax) then
2163 !     Special case with two 010's
2164         n = 2;
2165         ang(0) = -PHImin;
2166         ang(1) = PHImin;
2167         tab(0,0) = .false.
2168         tab(2,0) = .false.
2169         tab(0,1) = .false.
2170         tab(2,1) = .false.
2171         tab(1,0) = .true.
2172         tab(1,1) = .true.
2173       else if (PHImin .eq. PI) then
2174 !     Special case with one 010
2175         n = 1
2176         ang(0) = PI
2177         tab(0,0) = .false.
2178         tab(2,0) = .false.
2179         tab(1,0) = .true.
2180       else if (PHImax .eq. 0.) then
2181 !     Special case with one 010
2182         n = 1
2183         ang(0) = 0.
2184         tab(0,0) = .false.
2185         tab(2,0) = .false.
2186         tab(1,0) = .true.
2187       else
2188 !     Standard cases
2189         n = 0
2190         if (PHImin .gt. 0.) then
2191 !     Start of range (011)
2192           ang(n) = PHImin
2193           tab(0,n) = .false.
2194           tab(1,n) = .true.
2195           tab(2,n) = .true.
2196 !     End of range (110)
2197           ang(n+1) = -PHImin
2198           tab(0,n+1) = .true.
2199           tab(1,n+1) = .true.
2200           tab(2,n+1) = .false.
2201           n = n+2
2202         endif
2203         if (PHImax .lt. PI) then
2204 !     Start of range (011)
2205           ang(n) = -PHImax
2206           tab(0,n) = .false.
2207           tab(1,n) = .true.
2208           tab(2,n) = .true.
2209 !     End of range (110)
2210           ang(n+1) = PHImax
2211           tab(0,n+1) = .true.
2212           tab(1,n+1) = .true.
2213           tab(2,n+1) = .false.
2214           n = n+2
2215         endif
2216       endif
2217
2218       return
2219       end subroutine angles2tab
2220 !-----------------------------------------------------------------------------
2221       subroutine minmax_angles(x,y,z,r,n,ang,tab)
2222 !     When solutions do not exist, assume all angles
2223 !     are acceptable - i.e., initial geometry must be correct
2224 !      implicit none
2225
2226 !     Includes
2227 !      include 'COMMON.GEO'
2228 !      include 'COMMON.LOCMOVE'
2229
2230 !     Input arguments
2231       real(kind=8) :: x,y,z,r
2232
2233 !     Output arguments
2234       integer :: n
2235       real(kind=8),dimension(0:3) :: ang
2236       logical,dimension(0:2,0:3) :: tab
2237
2238 !     Local variables
2239       real(kind=8) :: num, denom, phi
2240       real(kind=8) :: Kmin, Kmax
2241       integer :: i
2242
2243
2244       num = x*x + y*y + z*z
2245       denom = x*x + y*y
2246       n = 0
2247       if (denom .gt. 0.) then
2248         phi = atan2(y,x)
2249         denom = 2.*r*sqrt(denom)
2250         num = num+r*r
2251         Kmin = (num - dmin2)/denom
2252         Kmax = (num - dmax2)/denom
2253
2254 !     Allowed values of K (else all angles are acceptable)
2255 !     -1 <= Kmin <  1
2256 !     -1 <  Kmax <= 1
2257         if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2258           Kmin = -flag
2259         else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2260           Kmin = PI
2261         else
2262           Kmin = acos(Kmin)
2263         endif
2264
2265         if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2266           Kmax = flag
2267         else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2268           Kmax = 0.
2269         else
2270           Kmax = acos(Kmax)
2271         endif
2272
2273         if (Kmax .lt. Kmin) Kmax = Kmin
2274
2275         call angles2tab(Kmin, Kmax, n, ang, tab)
2276
2277 !     Add phi and check that angles are within range (-PI,PI]
2278         do i=0,n-1
2279           ang(i) = ang(i)+phi
2280           if (ang(i) .le. -PI) then
2281             ang(i) = ang(i)+2.*PI
2282           else if (ang(i) .gt. PI) then
2283             ang(i) = ang(i)-2.*PI
2284           endif
2285         enddo
2286       endif
2287
2288       return
2289       end subroutine minmax_angles
2290 !-----------------------------------------------------------------------------
2291       subroutine construct_tab
2292 !     Take a_... and b_... values and produces the results res_...
2293 !     x_ang are assumed to be all different (diff > small)
2294 !     x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2295 !      implicit none
2296
2297 !     Includes
2298 !      include 'COMMON.LOCMOVE'
2299
2300 !     Local variables
2301       integer :: n_max,i,j,index
2302       logical :: done
2303       real(kind=8) :: phi
2304
2305
2306       n_max = a_n + b_n
2307       if (n_max .eq. 0) then
2308         res_n = 0
2309         return
2310       endif
2311
2312       do i=0,n_max-1
2313         do j=0,1
2314           res_tab(j,0,i) = .true.
2315           res_tab(j,2,i) = .true.
2316           res_tab(j,1,i) = .false.
2317         enddo
2318       enddo
2319
2320       index = 0
2321       phi = -flag
2322       done = .false.
2323       do while (.not.done)
2324         res_ang(index) = flag
2325
2326 !     Check a first...
2327         do i=0,a_n-1
2328           if ((a_ang(i)-phi).gt.small .and. &
2329                a_ang(i) .lt. res_ang(index)) then
2330 !     Found a lower angle
2331             res_ang(index) = a_ang(i)
2332 !     Copy the values from a_tab into res_tab(0,,)
2333             res_tab(0,0,index) = a_tab(0,i)
2334             res_tab(0,1,index) = a_tab(1,i)
2335             res_tab(0,2,index) = a_tab(2,i)
2336 !     Set default values for res_tab(1,,)
2337             res_tab(1,0,index) = .true.
2338             res_tab(1,1,index) = .false.
2339             res_tab(1,2,index) = .true.
2340           else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2341 !     Found an equal angle (can only be equal to a b_ang)
2342             res_tab(0,0,index) = a_tab(0,i)
2343             res_tab(0,1,index) = a_tab(1,i)
2344             res_tab(0,2,index) = a_tab(2,i)
2345           endif
2346         enddo
2347 !     ...then check b
2348         do i=0,b_n-1
2349           if ((b_ang(i)-phi).gt.small .and. &
2350                b_ang(i) .lt. res_ang(index)) then
2351 !     Found a lower angle
2352             res_ang(index) = b_ang(i)
2353 !     Copy the values from b_tab into res_tab(1,,)
2354             res_tab(1,0,index) = b_tab(0,i)
2355             res_tab(1,1,index) = b_tab(1,i)
2356             res_tab(1,2,index) = b_tab(2,i)
2357 !     Set default values for res_tab(0,,)
2358             res_tab(0,0,index) = .true.
2359             res_tab(0,1,index) = .false.
2360             res_tab(0,2,index) = .true.
2361           else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2362 !     Found an equal angle (can only be equal to an a_ang)
2363             res_tab(1,0,index) = b_tab(0,i)
2364             res_tab(1,1,index) = b_tab(1,i)
2365             res_tab(1,2,index) = b_tab(2,i)
2366           endif
2367         enddo
2368
2369         if (res_ang(index) .eq. flag) then
2370           res_n = index
2371           done = .true.
2372         else if (index .eq. n_max-1) then
2373           res_n = n_max
2374           done = .true.
2375         else
2376           phi = res_ang(index)  ! Store previous angle
2377           index = index+1
2378         endif
2379       enddo
2380
2381 !     Fill the gaps
2382 !     First a...
2383       index = 0
2384       if (a_n .gt. 0) then
2385         do while (.not.res_tab(0,1,index))
2386           index=index+1
2387         enddo
2388         done = res_tab(0,2,index)
2389         do i=index+1,res_n-1
2390           if (res_tab(0,1,i)) then
2391             done = res_tab(0,2,i)
2392           else
2393             res_tab(0,0,i) = done
2394             res_tab(0,1,i) = done
2395             res_tab(0,2,i) = done
2396           endif
2397         enddo
2398         done = res_tab(0,0,index)
2399         do i=index-1,0,-1
2400           if (res_tab(0,1,i)) then
2401             done = res_tab(0,0,i)
2402           else
2403             res_tab(0,0,i) = done
2404             res_tab(0,1,i) = done
2405             res_tab(0,2,i) = done
2406           endif
2407         enddo
2408       else
2409         do i=0,res_n-1
2410           res_tab(0,0,i) = .true.
2411           res_tab(0,1,i) = .true.
2412           res_tab(0,2,i) = .true.
2413         enddo
2414       endif
2415 !     ...then b
2416       index = 0
2417       if (b_n .gt. 0) then
2418         do while (.not.res_tab(1,1,index))
2419           index=index+1
2420         enddo
2421         done = res_tab(1,2,index)
2422         do i=index+1,res_n-1
2423           if (res_tab(1,1,i)) then
2424             done = res_tab(1,2,i)
2425           else
2426             res_tab(1,0,i) = done
2427             res_tab(1,1,i) = done
2428             res_tab(1,2,i) = done
2429           endif
2430         enddo
2431         done = res_tab(1,0,index)
2432         do i=index-1,0,-1
2433           if (res_tab(1,1,i)) then
2434             done = res_tab(1,0,i)
2435           else
2436             res_tab(1,0,i) = done
2437             res_tab(1,1,i) = done
2438             res_tab(1,2,i) = done
2439           endif
2440         enddo
2441       else
2442         do i=0,res_n-1
2443           res_tab(1,0,i) = .true.
2444           res_tab(1,1,i) = .true.
2445           res_tab(1,2,i) = .true.
2446         enddo
2447       endif
2448
2449 !     Finally fill the last row with AND operation
2450       do i=0,res_n-1
2451         do j=0,2
2452           res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2453         enddo
2454       enddo
2455
2456       return
2457       end subroutine construct_tab
2458 !-----------------------------------------------------------------------------
2459       subroutine construct_ranges(phi_n,phi_start,phi_end)
2460 !     Given the data in res_..., construct a table of
2461 !     min/max allowed angles
2462 !      implicit none
2463
2464 !     Includes
2465 !      include 'COMMON.GEO'
2466 !      include 'COMMON.LOCMOVE'
2467
2468 !     Output arguments
2469       integer :: phi_n
2470       real(kind=8),dimension(0:11) :: phi_start,phi_end
2471
2472 !     Local variables
2473       logical :: done
2474       integer :: index
2475
2476
2477       if (res_n .eq. 0) then
2478 !     Any move is allowed
2479         phi_n = 1
2480         phi_start(0) = -PI
2481         phi_end(0) = PI
2482       else
2483         phi_n = 0
2484         index = 0
2485         done = .false.
2486         do while (.not.done)
2487 !     Find start of range (01x)
2488           done = .false.
2489           do while (.not.done)
2490             if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2491               index=index+1
2492             else
2493               done = .true.
2494               phi_start(phi_n) = res_ang(index)
2495             endif
2496             if (index .eq. res_n) done = .true.
2497           enddo
2498 !     If a start was found (index < res_n), find the end of range (x10)
2499 !     It may not be found without wrapping around
2500           if (index .lt. res_n) then
2501             done = .false.
2502             do while (.not.done)
2503               if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2504                 index=index+1
2505               else
2506                 done = .true.
2507               endif
2508               if (index .eq. res_n) done = .true.
2509             enddo
2510             if (index .lt. res_n) then
2511 !     Found the end of the range
2512               phi_end(phi_n) = res_ang(index)
2513               phi_n=phi_n+1
2514               index=index+1
2515               if (index .eq. res_n) then
2516                 done = .true.
2517               else
2518                 done = .false.
2519               endif
2520             else
2521 !     Need to wrap around
2522               done = .true.
2523               phi_end(phi_n) = flag
2524             endif
2525           endif
2526         enddo
2527 !     Take care of the last one if need to wrap around
2528         if (phi_end(phi_n) .eq. flag) then
2529           index = 0
2530           do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2531             index=index+1
2532           enddo
2533           phi_end(phi_n) = res_ang(index) + 2.*PI
2534           phi_n=phi_n+1
2535         endif
2536       endif
2537
2538       return
2539       end subroutine construct_ranges
2540 !-----------------------------------------------------------------------------
2541       subroutine fix_no_moves(phi)
2542 !      implicit none
2543
2544 !     Includes
2545 !      include 'COMMON.GEO'
2546 !      include 'COMMON.LOCMOVE'
2547
2548 !     Output arguments
2549       real(kind=8) :: phi
2550
2551 !     Local variables
2552       integer :: index
2553       real(kind=8) :: diff,temp
2554
2555
2556 !     Look for first 01x in gammas (there MUST be at least one)
2557       diff = flag
2558       index = 0
2559       do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2560         index=index+1
2561       enddo
2562       if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2563 !     Try to increase PHImax
2564         if (index .gt. 0) then
2565           phi = res_ang(index-1)
2566           diff = abs(res_ang(index) - res_ang(index-1))
2567         endif
2568 !     Look for last (corresponding) x10
2569         index = res_n - 1
2570         do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2571           index=index-1
2572         enddo
2573         if (index .lt. res_n-1) then
2574           temp = abs(res_ang(index) - res_ang(index+1))
2575           if (temp .lt. diff) then
2576             phi = res_ang(index+1)
2577             diff = temp
2578           endif
2579         endif
2580       endif
2581
2582 !     If increasing PHImax didn't work, decreasing PHImin
2583 !     will (with one exception)
2584 !     Look for first x10 (there MUST be at least one)
2585       index = 0
2586       do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2587         index=index+1
2588       enddo
2589       if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2590 !     Try to decrease PHImin
2591         if (index .lt. res_n-1) then
2592           temp = abs(res_ang(index) - res_ang(index+1))
2593           if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2594             phi = res_ang(index+1)
2595             diff = temp
2596           endif
2597         endif
2598 !     Look for last (corresponding) 01x
2599         index = res_n - 1
2600         do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2601           index=index-1
2602         enddo
2603         if (index .gt. 0) then
2604           temp = abs(res_ang(index) - res_ang(index-1))
2605           if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2606             phi = res_ang(index-1)
2607             diff = temp
2608           endif
2609         endif
2610       endif
2611
2612 !     If it still didn't work, it must be PHImax == 0. or PHImin == PI
2613       if (diff .eq. flag) then
2614         index = 0
2615         if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2616              res_tab(index,1,2)) index = res_n - 1
2617 !     This MUST work at this point
2618         if (index .eq. 0) then
2619           phi = res_ang(1)
2620         else
2621           phi = res_ang(index - 1)
2622         endif
2623       endif
2624
2625       return
2626       end subroutine fix_no_moves
2627 !-----------------------------------------------------------------------------
2628       integer function move_res(PHImin,PHImax,i_move)
2629 !     Moves residue i_move (in array c), leaving everything else fixed
2630 !     Starting geometry is not checked, it should be correct!
2631 !     R(,i_move) is the only residue that will move, but must have
2632 !     1 < i_move < nres (i.e., cannot move ends)
2633 !     Whether any output is done is controlled by locmove_output
2634 !rc      implicit none
2635       use random,only:ran_number
2636 !     Includes
2637 !      implicit real*8 (a-h,o-z)
2638 !      include 'DIMENSIONS'
2639 !      include 'COMMON.CHAIN'
2640 !      include 'COMMON.GEO'
2641 !      include 'COMMON.LOCMOVE'
2642
2643 !     External functions
2644 !EL      double precision ran_number
2645 !EL      external ran_number
2646
2647 !     Input arguments
2648       real(kind=8) :: PHImin,PHImax
2649       integer :: i_move
2650
2651 !     RETURN VALUES:
2652 !     0: move successfull
2653 !     1: Dmin or Dmax had to be modified
2654 !     2: move failed - check your input geometry
2655
2656
2657 !     Local variables
2658       real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2659       real(kind=8),dimension(0:2) :: P
2660       logical :: no_moves,done
2661       integer :: index,i,j
2662       real(kind=8) :: phi,temp,radius
2663       real(kind=8),dimension(0:11) :: phi_start,phi_end
2664       integer :: phi_n
2665
2666 !     Set up the coordinate system
2667       do i=0,2
2668         Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2669       enddo
2670
2671       do i=0,2
2672         Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2673       enddo
2674       temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2675       do i=0,2
2676         Z(i)=Z(i)/temp
2677       enddo
2678
2679       do i=0,2
2680         X(i)=c(i+1,i_move)-Orig(i)
2681       enddo
2682 !     radius is the radius of the circle on which c(,i_move) can move
2683       radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2684       do i=0,2
2685         X(i)=X(i)/radius
2686       enddo
2687
2688       Y(0)=Z(1)*X(2)-X(1)*Z(2)
2689       Y(1)=X(0)*Z(2)-Z(0)*X(2)
2690       Y(2)=Z(0)*X(1)-X(0)*Z(1)
2691
2692 !     Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2693       if (i_move.gt.2) then
2694         do i=0,2
2695           P(i)=c(i+1,i_move-2)-Orig(i)
2696         enddo
2697         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2698              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2699              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2700              radius,a_n,a_ang,a_tab)
2701       else
2702         a_n=0
2703       endif
2704
2705 !     Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2706       if (i_move.lt.nres-2) then
2707         do i=0,2
2708           P(i)=c(i+1,i_move+2)-Orig(i)
2709         enddo
2710         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2711              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2712              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2713              radius,b_n,b_ang,b_tab)
2714       else
2715         b_n=0
2716       endif
2717
2718 !     Construct the resulting table for alpha and beta
2719       call construct_tab()
2720
2721       if (locmove_output) then
2722         print *,'ALPHAS & BETAS TABLE'
2723         call output_tabs()
2724       endif
2725
2726 !     Check that there is at least one possible move
2727       no_moves = .true.
2728       if (res_n .eq. 0) then
2729         no_moves = .false.
2730       else
2731         index = 0
2732         do while ((index .lt. res_n) .and. no_moves)
2733           if (res_tab(2,1,index)) no_moves = .false.
2734           index=index+1
2735         enddo
2736       endif
2737       if (no_moves) then
2738         if (locmove_output) print *,'   ***   Cannot move anywhere'
2739         move_res=2
2740         return
2741       endif
2742
2743 !     Transfer res_... into a_...
2744       a_n = 0
2745       do i=0,res_n-1
2746         if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2747              (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2748           a_ang(a_n) = res_ang(i)
2749           do j=0,2
2750             a_tab(j,a_n) = res_tab(2,j,i)
2751           enddo
2752           a_n=a_n+1
2753         endif
2754       enddo
2755
2756 !     Check that the PHI's are within [0,PI]
2757       if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2758       if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2759       if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2760       if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2761       if (PHImax .lt. PHImin) PHImax = PHImin
2762 !     Calculate min and max angles coming from PHImin and PHImax,
2763 !     and put them in b_...
2764       call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2765 !     Construct the final table
2766       call construct_tab()
2767
2768       if (locmove_output) then
2769         print *,'FINAL TABLE'
2770         call output_tabs()
2771       endif
2772
2773 !     Check that there is at least one possible move
2774       no_moves = .true.
2775       if (res_n .eq. 0) then
2776         no_moves = .false.
2777       else
2778         index = 0
2779         do while ((index .lt. res_n) .and. no_moves)
2780           if (res_tab(2,1,index)) no_moves = .false.
2781           index=index+1
2782         enddo
2783       endif
2784
2785       if (no_moves) then
2786 !     Take care of the case where no solution exists...
2787         call fix_no_moves(phi)
2788         if (locmove_output) then
2789           print *,'   ***   Had to modify PHImin or PHImax'
2790           print *,'phi: ',phi*rad2deg
2791         endif
2792         move_res=1
2793       else
2794 !     ...or calculate the solution
2795 !     Construct phi_start/phi_end arrays
2796         call construct_ranges(phi_n, phi_start, phi_end)
2797 !     Choose random angle phi in allowed range(s)
2798         temp = 0.
2799         do i=0,phi_n-1
2800           temp = temp + phi_end(i) - phi_start(i)
2801         enddo
2802         phi = ran_number(phi_start(0),phi_start(0)+temp)
2803         index = 0
2804         done = .false.
2805         do while (.not.done)
2806           if (phi .lt. phi_end(index)) then
2807             done = .true.
2808           else
2809             index=index+1
2810           endif
2811           if (index .eq. phi_n) then
2812             done = .true.
2813           else if (.not.done) then
2814             phi = phi + phi_start(index) - phi_end(index-1)
2815           endif
2816         enddo
2817         if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2818         if (phi .gt. PI) phi = phi-2.*PI
2819
2820         if (locmove_output) then
2821           print *,'ALLOWED RANGE(S)'
2822           do i=0,phi_n-1
2823             print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2824           enddo
2825           print *,'phi: ',phi*rad2deg
2826         endif
2827         move_res=0
2828       endif
2829
2830 !     Re-use radius as temp variable
2831       temp=radius*cos(phi)
2832       radius=radius*sin(phi)
2833       do i=0,2
2834         c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2835       enddo
2836
2837       return
2838       end function move_res
2839 !-----------------------------------------------------------------------------
2840       subroutine loc_test
2841 !rc      implicit none
2842
2843 !     Includes
2844 !      implicit real*8 (a-h,o-z)
2845 !      include 'DIMENSIONS'
2846 !      include 'COMMON.GEO'
2847 !      include 'COMMON.LOCAL'
2848 !      include 'COMMON.LOCMOVE'
2849
2850 !     External functions
2851 !EL      integer move_res
2852 !EL      external move_res
2853
2854 !     Local variables
2855       integer :: i,j,imov
2856       integer :: phi_n
2857       real(kind=8),dimension(0:11) :: phi_start,phi_end
2858       real(kind=8) :: phi
2859       real(kind=8),dimension(0:2,0:5) :: R
2860
2861       locmove_output=.true.
2862
2863 !      call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2864 !      call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2865 !      call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2866 !      call construct_tab
2867 !      call output_tabs
2868
2869 !      call construct_ranges(phi_n,phi_start,phi_end)
2870 !      do i=0,phi_n-1
2871 !        print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2872 !      enddo
2873
2874 !      call fix_no_moves(phi)
2875 !      print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2876
2877       R(0,0)=0.D0
2878       R(1,0)=0.D0
2879       R(2,0)=0.D0
2880       R(0,1)=0.D0
2881       R(1,1)=-cos(28.D0*deg2rad)
2882       R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2883       R(0,2)=0.D0
2884       R(1,2)=0.D0
2885       R(2,2)=-0.5D0
2886       R(0,3)=cos(30.D0*deg2rad)
2887       R(1,3)=0.D0
2888       R(2,3)=0.D0
2889       R(0,4)=0.D0
2890       R(1,4)=0.D0
2891       R(2,4)=0.5D0
2892       R(0,5)=0.D0
2893       R(1,5)=cos(26.D0*deg2rad)
2894       R(2,5)=0.5D0+sin(26.D0*deg2rad)
2895       do i=1,5
2896         do j=0,2
2897           R(j,i)=vbl*R(j,i)
2898         enddo
2899       enddo
2900 !      i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2901       imov=2
2902       i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2903       print *,'RETURNED ',i
2904       print *,(R(i,3)/vbl,i=0,2)
2905
2906       return
2907       end subroutine loc_test
2908 #endif
2909 !-----------------------------------------------------------------------------
2910 ! matmult.f
2911 !-----------------------------------------------------------------------------
2912       subroutine MATMULT(A1,A2,A3)
2913 !      implicit real*8 (a-h,o-z)
2914 !      include 'DIMENSIONS'
2915 !el local variables
2916       integer :: i,j,k
2917       real(kind=8) :: A3IJ
2918
2919       real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2920       real(kind=8),DIMENSION(3,3) :: AI3
2921       DO 1 I=1,3
2922         DO 2 J=1,3
2923           A3IJ=0.0
2924           DO 3 K=1,3
2925     3       A3IJ=A3IJ+A1(I,K)*A2(K,J)
2926           AI3(I,J)=A3IJ
2927     2   CONTINUE
2928     1 CONTINUE
2929       DO 4 I=1,3
2930       DO 4 J=1,3
2931     4   A3(I,J)=AI3(I,J)
2932       return
2933       end subroutine MATMULT
2934 !-----------------------------------------------------------------------------
2935 ! readpdb.F
2936 !-----------------------------------------------------------------------------
2937       subroutine int_from_cart(lside,lprn)
2938 !      implicit real*8 (a-h,o-z)
2939 !      include 'DIMENSIONS'
2940       use control_data,only:out1file
2941 #ifdef MPI
2942       include "mpif.h"
2943 #endif
2944 !      include 'COMMON.LOCAL'
2945 !      include 'COMMON.VAR'
2946 !      include 'COMMON.CHAIN'
2947 !      include 'COMMON.INTERACT'
2948 !      include 'COMMON.IOUNITS'
2949 !      include 'COMMON.GEO'
2950 !      include 'COMMON.NAMES'
2951 !      include 'COMMON.CONTROL'
2952 !      include 'COMMON.SETUP'
2953       character(len=3) :: seq,res
2954 !      character*5 atom
2955       character(len=80) :: card
2956       real(kind=8),dimension(3,20) :: sccor
2957       integer :: i,j,iti !el  rescode,
2958       logical :: lside,lprn
2959       real(kind=8) :: di,cosfac,sinfac
2960       integer :: nres2
2961       nres2=2*nres
2962
2963       if(me.eq.king.or..not.out1file)then
2964        if (lprn) then
2965         write (iout,'(/a)') &
2966         'Internal coordinates calculated from crystal structure.'
2967         if (lside) then
2968           write (iout,'(8a)') '  Res  ','       dvb','     Theta',&
2969        '     Gamma','    Dsc_id','       Dsc','     Alpha',&
2970        '     Beta '
2971         else
2972           write (iout,'(4a)') '  Res  ','       dvb','     Theta',&
2973        '     Gamma'
2974         endif
2975        endif
2976       endif
2977       do i=1,nres-1
2978 !       if (molnum(i).ne.1) cycle
2979 !in wham      do i=1,nres
2980         iti=itype(i,1)
2981         if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2982        (iti.ne.ntyp1  .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2983           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2984 !test          stop
2985         endif
2986 !#ifndef WHAM_RUN
2987         vbld(i+1)=dist(i,i+1)
2988         vbld_inv(i+1)=1.0d0/vbld(i+1)
2989 !#endif
2990         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2991         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2992       enddo
2993 !el -----
2994 !#ifdef WHAM_RUN
2995 !      if (itype(1,1).eq.ntyp1) then
2996 !        do j=1,3
2997 !          c(j,1)=c(j,2)+(c(j,3)-c(j,4))
2998 !        enddo
2999 !      endif
3000 !      if (itype(nres,1).eq.ntyp1) then
3001 !        do j=1,3
3002 !          c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
3003 !        enddo
3004 !      endif
3005 !#endif
3006 !      if (unres_pdb) then
3007 !        if (itype(1,1).eq.21) then
3008 !          theta(3)=90.0d0*deg2rad
3009 !          phi(4)=180.0d0*deg2rad
3010 !          vbld(2)=3.8d0
3011 !          vbld_inv(2)=1.0d0/vbld(2)
3012 !        endif
3013 !        if (itype(nres,1).eq.21) then
3014 !          theta(nres)=90.0d0*deg2rad
3015 !          phi(nres)=180.0d0*deg2rad
3016 !          vbld(nres)=3.8d0
3017 !          vbld_inv(nres)=1.0d0/vbld(2)
3018 !        endif
3019 !      endif
3020       if (lside) then
3021         do i=2,nres-1
3022           do j=1,3
3023             c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
3024            +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
3025 ! in wham            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
3026           enddo
3027           iti=itype(i,1)
3028           di=dist(i,nres+i)
3029 !#ifndef WHAM_RUN
3030 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3031
3032           if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3033            di=dsc(itype(i,molnum(i)))
3034           vbld(i+nres)=di
3035           if (itype(i,1).ne.10) then
3036             vbld_inv(i+nres)=1.0d0/di
3037           else
3038             vbld_inv(i+nres)=0.0d0
3039           endif
3040 !#endif
3041           if (iti.ne.10) then
3042             alph(i)=alpha(nres+i,i,nres2+2)
3043             omeg(i)=beta(nres+i,i,nres2+2,i+1)
3044           endif
3045           if (iti.ne.0) then
3046           if(me.eq.king.or..not.out1file)then
3047            if (lprn) &
3048            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3049            rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3050            rad2deg*alph(i),rad2deg*omeg(i)
3051           endif
3052           else
3053           if(me.eq.king.or..not.out1file)then
3054            if (lprn) &
3055            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3056            rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3057            rad2deg*alph(i),rad2deg*omeg(i)
3058           endif
3059           endif
3060         enddo
3061       else if (lprn) then
3062         do i=2,nres
3063           iti=itype(i,1)
3064           if(me.eq.king.or..not.out1file) &
3065            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3066            rad2deg*theta(i),rad2deg*phi(i)
3067         enddo
3068       endif
3069       return
3070       end subroutine int_from_cart
3071 !-----------------------------------------------------------------------------
3072       subroutine sc_loc_geom(lprn)
3073 !      implicit real*8 (a-h,o-z)
3074 !      include 'DIMENSIONS'
3075       use control_data,only:out1file
3076 #ifdef MPI
3077       include "mpif.h"
3078 #endif
3079 !      include 'COMMON.LOCAL'
3080 !      include 'COMMON.VAR'
3081 !      include 'COMMON.CHAIN'
3082 !      include 'COMMON.INTERACT'
3083 !      include 'COMMON.IOUNITS'
3084 !      include 'COMMON.GEO'
3085 !      include 'COMMON.NAMES'
3086 !      include 'COMMON.CONTROL'
3087 !      include 'COMMON.SETUP'
3088       real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3089       logical :: lprn
3090 !el local variables
3091       integer :: i,j,it,iti
3092       real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3093       do i=1,nres-1
3094         do j=1,3
3095           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3096         enddo
3097       enddo
3098       do i=2,nres-1
3099         if (itype(i,1).ne.10) then
3100           do j=1,3
3101             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3102           enddo
3103         else
3104           do j=1,3
3105             dc_norm(j,i+nres)=0.0d0
3106           enddo
3107         endif
3108       enddo
3109       do i=2,nres-1
3110         costtab(i+1) =dcos(theta(i+1))
3111         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3112         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3113         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3114         cosfac2=0.5d0/(1.0d0+costtab(i+1))
3115         cosfac=dsqrt(cosfac2)
3116         sinfac2=0.5d0/(1.0d0-costtab(i+1))
3117         sinfac=dsqrt(sinfac2)
3118         it=itype(i,1)
3119
3120         if ((it.ne.10).and.(it.ne.ntyp1)) then
3121 !el        if (it.ne.10) then
3122 !
3123 !  Compute the axes of tghe local cartesian coordinates system; store in
3124 !   x_prime, y_prime and z_prime
3125 !
3126         do j=1,3
3127           x_prime(j) = 0.00
3128           y_prime(j) = 0.00
3129           z_prime(j) = 0.00
3130         enddo
3131         do j = 1,3
3132           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3133           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3134         enddo
3135         call vecpr(x_prime,y_prime,z_prime)
3136 !
3137 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3138 ! to local coordinate system. Store in xx, yy, zz.
3139 !
3140         xx=0.0d0
3141         yy=0.0d0
3142         zz=0.0d0
3143         do j = 1,3
3144           xx = xx + x_prime(j)*dc_norm(j,i+nres)
3145           yy = yy + y_prime(j)*dc_norm(j,i+nres)
3146           zz = zz + z_prime(j)*dc_norm(j,i+nres)
3147         enddo
3148
3149         xxref(i)=xx
3150         yyref(i)=yy
3151         zzref(i)=zz
3152         else
3153         xxref(i)=0.0d0
3154         yyref(i)=0.0d0
3155         zzref(i)=0.0d0
3156         endif
3157       enddo
3158       if (lprn) then
3159         do i=2,nres
3160           iti=itype(i,1)
3161           if(me.eq.king.or..not.out1file) &
3162            write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3163             yyref(i),zzref(i)
3164         enddo
3165       endif
3166
3167       return
3168       end subroutine sc_loc_geom
3169 !-----------------------------------------------------------------------------
3170       subroutine sccenter(ires,nscat,sccor)
3171 !      implicit real*8 (a-h,o-z)
3172 !      include 'DIMENSIONS'
3173 !      include 'COMMON.CHAIN'
3174       integer :: i,j,ires,nscat
3175       real(kind=8),dimension(3,20) :: sccor
3176       real(kind=8) :: sccmj
3177 !        print *,"I am in sccenter",ires,nscat
3178       do j=1,3
3179         sccmj=0.0D0
3180         do i=1,nscat
3181           sccmj=sccmj+sccor(j,i)
3182 !C          print *,"insccent", ires,sccor(j,i)
3183         enddo
3184         dc(j,ires)=sccmj/nscat
3185       enddo
3186       return
3187       end subroutine sccenter
3188 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3189 !-----------------------------------------------------------------------------
3190       subroutine bond_regular
3191       use calc_data
3192 !      implicit real*8 (a-h,o-z)
3193 !      include 'DIMENSIONS'
3194 !      include 'COMMON.VAR'
3195 !      include 'COMMON.LOCAL'
3196 !      include 'COMMON.CALC'
3197 !      include 'COMMON.INTERACT'
3198 !      include 'COMMON.CHAIN'
3199       do i=1,nres-1
3200
3201        vbld(i+1)=vbl
3202        vbld_inv(i+1)=1.0d0/vbld(i+1)
3203        vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3204        vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3205 !       print *,vbld(i+1),vbld(i+1+nres)
3206       enddo
3207       return
3208       end subroutine bond_regular
3209 #endif
3210 !-----------------------------------------------------------------------------
3211 ! refsys.f
3212 !-----------------------------------------------------------------------------
3213       subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3214 ! This subroutine calculates unit vectors of a local reference system
3215 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3216 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3217 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3218 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3219 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3220 ! form a linear fragment. Returns vectors e1, e2, and e3.
3221 !      implicit real*8 (a-h,o-z)
3222 !      include 'DIMENSIONS'
3223       logical :: fail
3224       real(kind=8),dimension(3) :: e1,e2,e3
3225       real(kind=8),dimension(3) :: u,z
3226 !      include 'COMMON.IOUNITS'
3227 !      include 'COMMON.CHAIN'
3228       real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3229 !el local variables
3230       integer :: i,i1,i2,i3,i4
3231       real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3232       fail=.false.
3233       s1=0.0
3234       s2=0.0
3235       do 1 i=1,3
3236       zi=c(i,i2)-c(i,i3)
3237       ui=c(i,i4)-c(i,i3)
3238       s1=s1+zi*zi
3239       s2=s2+ui*ui
3240       z(i)=zi
3241     1 u(i)=ui
3242       s1=sqrt(s1)
3243       s2=sqrt(s2)
3244       if (s1.gt.coinc) goto 2
3245       write (iout,1000) i2,i3,i1
3246       fail=.true.
3247 !     do 3 i=1,3
3248 !   3 c(i,i1)=0.0D0
3249       return
3250     2 if (s2.gt.coinc) goto 4
3251       write(iout,1000) i3,i4,i1
3252       fail=.true.
3253       do 5 i=1,3
3254     5 c(i,i1)=0.0D0
3255       return
3256     4 s1=1.0/s1
3257       s2=1.0/s2
3258       v1=z(2)*u(3)-z(3)*u(2)
3259       v2=z(3)*u(1)-z(1)*u(3)
3260       v3=z(1)*u(2)-z(2)*u(1)
3261       anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3262       if (anorm.gt.align) goto 6
3263       write (iout,1010) i2,i3,i4,i1
3264       fail=.true.
3265 !     do 7 i=1,3
3266 !   7 c(i,i1)=0.0D0
3267       return
3268     6 anorm=1.0D0/anorm
3269       e3(1)=v1*anorm
3270       e3(2)=v2*anorm
3271       e3(3)=v3*anorm
3272       e1(1)=z(1)*s1
3273       e1(2)=z(2)*s1
3274       e1(3)=z(3)*s1
3275       e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3276       e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3277       e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3278  1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3279        'coordinates of atom',i4,' are set to zero.')
3280  1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3281        ' fragment. coordinates of atom',i4,' are set to zero.')
3282       return
3283       end subroutine refsys
3284 !-----------------------------------------------------------------------------
3285 ! int_to_cart.f
3286 !-----------------------------------------------------------------------------
3287       subroutine int_to_cart
3288 !--------------------------------------------------------------
3289 !  This subroutine converts the energy derivatives from internal
3290 !  coordinates to cartesian coordinates
3291 !-------------------------------------------------------------
3292 !      implicit real*8 (a-h,o-z)
3293 !      include 'DIMENSIONS'
3294 !      include 'COMMON.VAR'
3295 !      include 'COMMON.CHAIN'
3296 !      include 'COMMON.DERIV'
3297 !      include 'COMMON.GEO'
3298 !      include 'COMMON.LOCAL'
3299 !      include 'COMMON.INTERACT'
3300 !      include 'COMMON.MD'
3301 !      include 'COMMON.IOUNITS'
3302 !      include 'COMMON.SCCOR'
3303 !   calculating dE/ddc1
3304 !el local variables
3305        integer :: j,i
3306 !       print *,"gloc",gloc(:,:)
3307 !       print *, "gcart",gcart(:,:)
3308        if (nres.lt.3) go to 18
3309        do j=1,3
3310          gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3311            +gloc(nres-2,icg)*dtheta(j,1,3)
3312           if ((itype(2,1).ne.10).and.&
3313           (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3314           gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3315           gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3316         endif
3317        enddo
3318 !     Calculating the remainder of dE/ddc2
3319        do j=1,3
3320          gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3321          gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3322         if(itype(2,1).ne.10) then
3323           gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3324           gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3325         endif
3326         if(itype(3,1).ne.10) then
3327           gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3328           gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3329         endif
3330         if(nres.gt.4) then
3331           gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3332         endif
3333        enddo
3334 !  If there are only five residues
3335        if(nres.eq.5) then
3336          do j=1,3
3337            gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3338            dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3339            dtheta(j,1,5)
3340 !         if(itype(3,1).ne.10) then
3341           if ((itype(3,1).ne.10).and.&
3342           (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3343            gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3344            dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3345          endif
3346 !        if(itype(4,1).ne.10) then
3347           if ((itype(4,1).ne.10).and.&
3348           (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3349            gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3350            dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3351          endif
3352         enddo
3353        endif
3354 !    If there are more than five residues
3355       if(nres.gt.5) then
3356         do i=3,nres-3
3357          do j=1,3
3358           gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3359           +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3360           gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3361           gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3362           if(itype(i,1).ne.10) then
3363            gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3364            gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3365           endif
3366           if(itype(i+1,1).ne.10) then
3367            gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3368            +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3369           endif
3370          enddo
3371         enddo
3372       endif
3373 !  Setting dE/ddnres-2
3374       if(nres.gt.5) then
3375          do j=1,3
3376            gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3377            dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3378            +gloc(2*nres-6,icg)* &
3379            dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3380           if(itype(nres-2,1).ne.10) then
3381               gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3382               dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3383               domega(j,2,nres-2)
3384           endif
3385           if(itype(nres-1,1).ne.10) then
3386              gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3387              dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3388              domega(j,1,nres-1)
3389           endif
3390          enddo
3391       endif
3392 !  Settind dE/ddnres-1
3393 !#define DEBUG
3394 #ifdef DEBUG
3395           j=1
3396               write(iout,*)"in int to carta",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3397         gloc(2*nres-5,icg),dtheta(j,2,nres)
3398
3399 #endif
3400 !#undef DEBUG
3401
3402        do j=1,3
3403         gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3404         gloc(2*nres-5,icg)*dtheta(j,2,nres)
3405 !#define DEBUG
3406 #ifdef DEBUG
3407               write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3408         gloc(2*nres-5,icg),dtheta(j,2,nres)
3409
3410 #endif
3411 !#undef DEBUG
3412         if(itype(nres-1,1).ne.10) then
3413           gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3414           dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3415           domega(j,2,nres-1)
3416 !#define DEBUG
3417 #ifdef DEBUG
3418               write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3419           dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3420           domega(j,2,nres-1)
3421
3422 #endif
3423 !#undef DEBUG
3424
3425         endif
3426         enddo
3427 !   The side-chain vector derivatives
3428         do i=2,nres-1
3429          if(itype(i,1).ne.10 .and.  &
3430            itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3431             do j=1,3
3432               gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3433               +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3434 !#define DEBUG
3435 #ifdef DEBUG
3436               write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3437               gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3438 #endif
3439 !#undef DEBUG
3440             enddo
3441          endif
3442        enddo
3443 !----------------------------------------------------------------------
3444 ! INTERTYP=1 SC...Ca...Ca...Ca
3445 ! INTERTYP=2 Ca...Ca...Ca...SC
3446 ! INTERTYP=3 SC...Ca...Ca...SC
3447 !   calculating dE/ddc1
3448   18   continue
3449 !       do i=1,nres
3450 !       gloc(i,icg)=0.0D0
3451 !          write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3452 !       enddo
3453        if (nres.lt.2) return
3454        if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3455        if ((itype(1,1).ne.10).and. &
3456         (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3457         do j=1,3
3458 !c Derviative was calculated for oposite vector of side chain therefore
3459 ! there is "-" sign before gloc_sc
3460          gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3461            dtauangle(j,1,1,3)
3462          gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3463            dtauangle(j,1,2,3)
3464           if ((itype(2,1).ne.10).and. &
3465         (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3466          gxcart(j,1)= gxcart(j,1) &
3467                      -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3468          gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3469             dtauangle(j,3,2,3)
3470           endif
3471        enddo
3472        endif
3473          if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3474          (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3475       then
3476          do j=1,3
3477          gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3478          enddo
3479          endif
3480 !   As potetnial DO NOT depend on omicron anlge their derivative is
3481 !   ommited
3482 !     &     +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3483
3484 !     Calculating the remainder of dE/ddc2
3485        do j=1,3
3486          if((itype(2,1).ne.10).and. &
3487            (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3488            if ((itype(1,1).ne.10).and.&
3489               ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))))&
3490             gxcart(j,2)=gxcart(j,2)+ &
3491                                gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3492         if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3493          then
3494            gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3495 !c                  the   - above is due to different vector direction
3496            gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3497           endif
3498           if (nres.gt.3) then
3499 !           if ((itype(1,1).ne.10).and.&
3500 !              ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3501            gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3502 !c                  the   - above is due to different vector direction
3503            gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3504 !          write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3505 !           write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3506           endif
3507          endif
3508          if ((itype(1,1).ne.10).and.&
3509          (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3510           gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3511 !           write(iout,*)  gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3512         endif
3513          if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3514           gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3515 !           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3516          endif
3517          if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3518           gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3519 !           write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3520          endif
3521
3522 !      write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3523        enddo
3524 !    If there are more than five residues
3525       if(nres.ge.5) then
3526         do i=3,nres-2
3527          do j=1,3
3528 !          write(iout,*) "before", gcart(j,i)
3529           if ((itype(i,1).ne.10).and.&
3530           (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3531           gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3532           *dtauangle(j,2,3,i+1) &
3533           -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3534           gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3535           *dtauangle(j,1,2,i+2)
3536 !                   write(iout,*) "new",j,i,
3537 !     &  gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3538 !          if (itype(i-1,1).ne.10) then
3539           if ((itype(i-1,1).ne.10).and.&
3540           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3541
3542            gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3543       *dtauangle(j,3,3,i+1)
3544           endif
3545 !          if (itype(i+1,1).ne.10) then
3546           if ((itype(i+1,1).ne.10).and.&
3547           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3548           gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3549       *dtauangle(j,3,1,i+2)
3550            gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3551       *dtauangle(j,3,2,i+2)
3552           endif
3553           endif
3554 !          if (itype(i-1,1).ne.10) then
3555           if ((itype(i-1,1).ne.10).and.&
3556           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3557            gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3558            dtauangle(j,1,3,i+1)
3559           endif
3560 !          if (itype(i+1,1).ne.10) then
3561           if ((itype(i+1,1).ne.10).and.&
3562           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3563            gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3564            dtauangle(j,2,2,i+2)
3565 !          write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3566 !     &    dtauangle(j,2,2,i+2)
3567           endif
3568 !          if (itype(i+2,1).ne.10) then
3569           if ((itype(i+2,1).ne.10).and.&
3570           (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3571            gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3572            dtauangle(j,2,1,i+3)
3573           endif
3574          enddo
3575         enddo
3576       endif
3577 !  Setting dE/ddnres-1
3578       if(nres.ge.4) then
3579          do j=1,3
3580          if ((itype(nres-1,1).ne.10).and.&
3581        (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3582          gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3583           *dtauangle(j,2,3,nres)
3584 !          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3585 !     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
3586 !         if (itype(nres-2,1).ne.10) then
3587          if ((itype(nres-2,1).ne.10).and.&
3588        (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3589        gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3590           *dtauangle(j,3,3,nres)
3591           endif
3592          if ((itype(nres,1).ne.10).and.&
3593          (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3594         gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3595           *dtauangle(j,3,1,nres+1)
3596         gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3597           *dtauangle(j,3,2,nres+1)
3598           endif
3599          endif
3600          if ((itype(nres-2,1).ne.10).and.&
3601          (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3602             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3603          dtauangle(j,1,3,nres)
3604          endif
3605           if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3606             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3607            dtauangle(j,2,2,nres+1)
3608 !           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3609 !     &     dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3610            endif
3611          enddo
3612       endif
3613 !  Settind dE/ddnres
3614        if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3615           (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3616        do j=1,3
3617         gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3618        *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3619        *dtauangle(j,2,3,nres+1)
3620         enddo
3621        endif
3622 !   The side-chain vector derivatives
3623 !       print *,"gcart",gcart(:,:)
3624       return
3625       end subroutine int_to_cart
3626 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3627 !-----------------------------------------------------------------------------
3628 ! readrtns_CSA.F
3629 !-----------------------------------------------------------------------------
3630       subroutine gen_dist_constr
3631 ! Generate CA distance constraints.
3632 !      implicit real*8 (a-h,o-z)
3633 !      include 'DIMENSIONS'
3634 !      include 'COMMON.IOUNITS'
3635 !      include 'COMMON.GEO'
3636 !      include 'COMMON.VAR'
3637 !      include 'COMMON.INTERACT'
3638 !      include 'COMMON.LOCAL'
3639 !      include 'COMMON.NAMES'
3640 !      include 'COMMON.CHAIN'
3641 !      include 'COMMON.FFIELD'
3642 !      include 'COMMON.SBRIDGE'
3643 !      include 'COMMON.HEADER'
3644 !      include 'COMMON.CONTROL'
3645 !      include 'COMMON.DBASE'
3646 !      include 'COMMON.THREAD'
3647 !      include 'COMMON.TIME1'
3648 !      integer :: itype_pdb !(maxres)
3649 !      common /pizda/ itype_pdb(nres)
3650       character(len=2) :: iden
3651 !el local variables
3652       integer :: i,j
3653 !d      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3654 !d      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3655 !d     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3656 !d     & ' nsup',nsup
3657       do i=nstart_sup,nstart_sup+nsup-1
3658 !d      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3659 !d     &    ' seq_pdb', restyp(itype_pdb(i))
3660         do j=i+2,nstart_sup+nsup-1
3661           nhpb=nhpb+1
3662           ihpb(nhpb)=i+nstart_seq-nstart_sup
3663           jhpb(nhpb)=j+nstart_seq-nstart_sup
3664           forcon(nhpb)=weidis
3665           dhpb(nhpb)=dist(i,j)
3666         enddo
3667       enddo
3668 !d      write (iout,'(a)') 'Distance constraints:'
3669 !d      do i=nss+1,nhpb
3670 !d        ii=ihpb(i)
3671 !d        jj=jhpb(i)
3672 !d        iden='CA'
3673 !d        if (ii.gt.nres) then
3674 !d          iden='SC'
3675 !d          ii=ii-nres
3676 !d          jj=jj-nres
3677 !d        endif
3678 !d        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3679 !d     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3680 !d     &  dhpb(i),forcon(i)
3681 !d      enddo
3682 !      deallocate(itype_pdb)
3683
3684       return
3685       end subroutine gen_dist_constr
3686 #endif
3687 !-----------------------------------------------------------------------------
3688 ! cartprint.f
3689 !-----------------------------------------------------------------------------
3690       subroutine cartprint
3691
3692       use geometry_data, only: c
3693       use energy_data, only: itype
3694 !      implicit real*8 (a-h,o-z)
3695 !      include 'DIMENSIONS'
3696 !      include 'COMMON.CHAIN'
3697 !      include 'COMMON.INTERACT'
3698 !      include 'COMMON.NAMES'
3699 !      include 'COMMON.IOUNITS'
3700       integer :: i
3701
3702       write (iout,100)
3703       do i=1,nres
3704         write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3705           c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3706       enddo
3707   100 format (//'              alpha-carbon coordinates       ',&
3708                 '     centroid coordinates'/ &
3709                 '       ', 6X,'X',11X,'Y',11X,'Z',&
3710                                 10X,'X',11X,'Y',11X,'Z')
3711   110 format (a,'(',i3,')',6f12.5)
3712       return
3713       end subroutine cartprint
3714 !-----------------------------------------------------------------------------
3715 !-----------------------------------------------------------------------------
3716       subroutine alloc_geo_arrays
3717 !EL Allocation of tables used by module energy
3718
3719       integer :: i,j,nres2
3720       nres2=2*nres
3721 ! commom.bounds
3722 !      common /bounds/
3723       allocate(phibound(2,nres+2)) !(2,maxres)
3724 !----------------------
3725 ! commom.chain
3726 !      common /chain/ in molread
3727 !      real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3728 !      real(kind=8),dimension(:,:),allocatable :: dc
3729       allocate(dc_old(3,0:nres2))
3730 !      if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3731       if(.not.allocated(dc_norm2)) then
3732         allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3733         dc_norm2(:,:)=0.d0
3734       endif
3735 !
3736 !el      if(.not.allocated(dc_norm))
3737 !elwrite(iout,*) "jestem w alloc geo 1"
3738       if(.not.allocated(dc_norm)) then
3739         allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3740         dc_norm(:,:)=0.d0
3741       endif
3742 !elwrite(iout,*) "jestem w alloc geo 1"
3743       allocate(xloc(3,nres),xrot(3,nres))
3744 !elwrite(iout,*) "jestem w alloc geo 1"
3745       xloc(:,:)=0.0D0
3746 !elwrite(iout,*) "jestem w alloc geo 1"
3747       allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3748 !      common /rotmat/
3749       allocate(t(3,3,nres),r(3,3,nres))
3750       allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3751 !      common /refstruct/
3752       if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3753 !elwrite(iout,*) "jestem w alloc geo 2"
3754       allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3755       if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3756       if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3757 !      common /from_zscore/ in module.compare
3758 !----------------------
3759 ! common.local
3760 ! Inverses of the actual virtual bond lengths
3761 !      common /invlen/ in io_conf: molread or readpdb
3762 !      real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3763 !----------------------
3764 ! common.var
3765 ! Store the geometric variables in the following COMMON block.
3766 !      common /var/ in readpdb or ...
3767       if(.not.allocated(theta)) allocate(theta(nres+2))
3768       if(.not.allocated(phi)) allocate(phi(nres+2))
3769       if(.not.allocated(alph)) allocate(alph(nres+2))
3770       if(.not.allocated(omeg)) allocate(omeg(nres+2))
3771       if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3772       if(.not.allocated(phiref)) allocate(phiref(nres+2))
3773       if(.not.allocated(costtab)) allocate(costtab(nres))
3774       if(.not.allocated(sinttab)) allocate(sinttab(nres))
3775       if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3776       if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3777 !      real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3778       allocate(omicron(2,nres+2)) !(2,maxres)
3779       allocate(tauangle(3,nres+2)) !(3,maxres)
3780 !elwrite(iout,*) "jestem w alloc geo 3"
3781       if(.not.allocated(xxtab)) allocate(xxtab(nres))
3782       if(.not.allocated(yytab)) allocate(yytab(nres))
3783       if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3784       if(.not.allocated(xxref)) allocate(xxref(nres))
3785       if(.not.allocated(yyref)) allocate(yyref(nres))
3786       if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3787       allocate(ialph(nres,2)) !(maxres,2)
3788       ialph(:,1)=0
3789       ialph(:,2)=0
3790       allocate(ivar(4*nres2)) !(4*maxres2)
3791
3792 #if defined(WHAM_RUN) || defined(CLUSTER)
3793       allocate(vbld(2*nres))
3794       vbld(:)=0.d0
3795       allocate(vbld_inv(2*nres))
3796       vbld_inv(:)=0.d0
3797 #endif
3798
3799       return
3800       end subroutine alloc_geo_arrays
3801 !-----------------------------------------------------------------------------
3802 !-----------------------------------------------------------------------------
3803       subroutine returnbox
3804       integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3805       integer :: chain_end,ireturnval
3806       real*8 :: difference
3807 !C change suggested by Ana - end
3808         j=1
3809         chain_beg=1
3810 !C        do i=1,nres
3811 !C       write(*,*) 'initial', i,j,c(j,i)
3812 !C        enddo
3813 !C change suggested by Ana - begin
3814         allareout=1
3815 !C change suggested by Ana -end
3816         do i=1,nres-1
3817            mnum=molnum(i)
3818          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3819             .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3820           chain_end=i
3821           if (allareout.eq.1) then
3822             ireturnval=int(c(j,i)/boxxsize)
3823             if (c(j,i).le.0) ireturnval=ireturnval-1
3824             do k=chain_beg,chain_end
3825               c(j,k)=c(j,k)-ireturnval*boxxsize
3826               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3827             enddo
3828 !C Suggested by Ana
3829             if (chain_beg.eq.1) &
3830             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3831 !C Suggested by Ana -end
3832            endif
3833            chain_beg=i+1
3834            allareout=1
3835          else
3836           if (int(c(j,i)/boxxsize).eq.0) allareout=0
3837          endif
3838         enddo
3839          if (allareout.eq.1) then
3840             ireturnval=int(c(j,i)/boxxsize)
3841             if (c(j,i).le.0) ireturnval=ireturnval-1
3842             do k=chain_beg,nres
3843               c(j,k)=c(j,k)-ireturnval*boxxsize
3844               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3845             enddo
3846           endif
3847 !C NO JUMP
3848 !C        do i=1,nres
3849 !C        write(*,*) 'befor no jump', i,j,c(j,i)
3850 !C        enddo
3851         nojumpval=0
3852         do i=2,nres
3853            mnum=molnum(i)
3854            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3855               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3856              difference=abs(c(j,i-1)-c(j,i))
3857 !C             print *,'diff', difference
3858              if (difference.gt.boxxsize/2.0) then
3859                 if (c(j,i-1).gt.c(j,i)) then
3860                   nojumpval=1
3861                  else
3862                    nojumpval=-1
3863                  endif
3864               else
3865               nojumpval=0
3866               endif
3867               endif
3868               c(j,i)=c(j,i)+nojumpval*boxxsize
3869               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3870          enddo
3871        nojumpval=0
3872         do i=2,nres
3873            mnum=molnum(i)
3874            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3875              difference=abs(c(j,i-1)-c(j,i))
3876              if (difference.gt.boxxsize/2.0) then
3877                 if (c(j,i-1).gt.c(j,i)) then
3878                   nojumpval=1
3879                  else
3880                    nojumpval=-1
3881                  endif
3882               else
3883               nojumpval=0
3884               endif
3885              endif
3886               c(j,i)=c(j,i)+nojumpval*boxxsize
3887               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3888          enddo
3889
3890 !C        do i=1,nres
3891 !C        write(*,*) 'after no jump', i,j,c(j,i)
3892 !C        enddo
3893
3894 !C NOW Y dimension
3895 !C suggesed by Ana begins
3896         allareout=1
3897         j=2
3898         chain_beg=1
3899         do i=1,nres-1
3900            mnum=molnum(i)
3901          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3902            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3903           chain_end=i
3904           if (allareout.eq.1) then
3905             ireturnval=int(c(j,i)/boxysize)
3906             if (c(j,i).le.0) ireturnval=ireturnval-1
3907             do k=chain_beg,chain_end
3908               c(j,k)=c(j,k)-ireturnval*boxysize
3909              c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3910             enddo
3911 !C Suggested by Ana
3912             if (chain_beg.eq.1) &
3913             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3914 !C Suggested by Ana -end
3915            endif
3916            chain_beg=i+1
3917            allareout=1
3918          else
3919           if (int(c(j,i)/boxysize).eq.0) allareout=0
3920          endif
3921         enddo
3922          if (allareout.eq.1) then
3923             ireturnval=int(c(j,i)/boxysize)
3924             if (c(j,i).le.0) ireturnval=ireturnval-1
3925             do k=chain_beg,nres
3926               c(j,k)=c(j,k)-ireturnval*boxysize
3927               c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3928             enddo
3929           endif
3930         nojumpval=0
3931         do i=2,nres
3932            mnum=molnum(i)
3933            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3934               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3935              difference=abs(c(j,i-1)-c(j,i))
3936              if (difference.gt.boxysize/2.0) then
3937                 if (c(j,i-1).gt.c(j,i)) then
3938                   nojumpval=1
3939                  else
3940                    nojumpval=-1
3941                  endif
3942              else
3943               nojumpval=0
3944               endif
3945            endif
3946               c(j,i)=c(j,i)+nojumpval*boxysize
3947               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3948          enddo
3949       nojumpval=0
3950         do i=2,nres
3951            mnum=molnum(i)
3952            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3953              .and. itype(i-1,mnum).eq.ntyp1) then
3954              difference=abs(c(j,i-1)-c(j,i))
3955              if (difference.gt.boxysize/2.0) then
3956                 if (c(j,i-1).gt.c(j,i)) then
3957                   nojumpval=1
3958                  else
3959                    nojumpval=-1
3960                  endif
3961               else
3962               nojumpval=0
3963               endif
3964             endif
3965               c(j,i)=c(j,i)+nojumpval*boxysize
3966               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3967          enddo
3968 !C Now Z dimension
3969 !C Suggested by Ana -begins
3970         allareout=1
3971 !C Suggested by Ana -ends
3972        j=3
3973         chain_beg=1
3974         do i=1,nres-1
3975            mnum=molnum(i)
3976          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3977            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3978           chain_end=i
3979           if (allareout.eq.1) then
3980             ireturnval=int(c(j,i)/boxysize)
3981             if (c(j,i).le.0) ireturnval=ireturnval-1
3982             do k=chain_beg,chain_end
3983               c(j,k)=c(j,k)-ireturnval*boxzsize
3984               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3985             enddo
3986 !C Suggested by Ana
3987             if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3988 !C Suggested by Ana -end
3989            endif
3990            chain_beg=i+1
3991            allareout=1
3992          else
3993           if (int(c(j,i)/boxzsize).eq.0) allareout=0
3994          endif
3995         enddo
3996          if (allareout.eq.1) then
3997             ireturnval=int(c(j,i)/boxzsize)
3998             if (c(j,i).le.0) ireturnval=ireturnval-1
3999             do k=chain_beg,nres
4000               c(j,k)=c(j,k)-ireturnval*boxzsize
4001               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
4002             enddo
4003           endif
4004         nojumpval=0
4005         do i=2,nres
4006            mnum=molnum(i)
4007            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4008              difference=abs(c(j,i-1)-c(j,i))
4009              if (difference.gt.(boxzsize/2.0)) then
4010                 if (c(j,i-1).gt.c(j,i)) then
4011                   nojumpval=1
4012                  else
4013                    nojumpval=-1
4014                  endif
4015               else
4016               nojumpval=0
4017               endif
4018             endif
4019               c(j,i)=c(j,i)+nojumpval*boxzsize
4020               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4021          enddo
4022        nojumpval=0
4023         do i=2,nres
4024            mnum=molnum(i)
4025            if (itype(i,mnum).eq.ntyp1_molec(mnum) &
4026             .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
4027              difference=abs(c(j,i-1)-c(j,i))
4028              if (difference.gt.boxzsize/2.0) then
4029                 if (c(j,i-1).gt.c(j,i)) then
4030                   nojumpval=1
4031                  else
4032                    nojumpval=-1
4033                  endif
4034               else
4035               nojumpval=0
4036               endif
4037             endif
4038              c(j,i)=c(j,i)+nojumpval*boxzsize
4039               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4040          enddo
4041         do i=1,nres
4042          if (molnum(i).eq.5) then
4043           c(1,i)=dmod(c(1,i),boxxsize)
4044           c(2,i)=dmod(c(2,i),boxysize)
4045           c(3,i)=dmod(c(3,i),boxzsize)
4046           c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4047           c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4048           c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4049          endif
4050         enddo
4051         return
4052         end       subroutine returnbox
4053 !-------------------------------------------------------------------------------------------------------
4054       end module geometry