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