source/unres/geometry.F90

   1                       module geometry
   2 !-----------------------------------------------------------------------------
   3       use io_units
   4       use names
   5       use math
   6       use MPI_data
   7       use geometry_data
   8       use control_data
   9       use energy_data
  10       implicit none
  11 !-----------------------------------------------------------------------------
  12 ! commom.bounds
  13 !      common /bounds/
  14 !-----------------------------------------------------------------------------
  15 ! commom.chain
  16 !      common /chain/
  17 !      common /rotmat/
  18       real(kind=8),dimension(:,:,:),allocatable :: t,r !(3,3,maxres)
  19 !-----------------------------------------------------------------------------
  20 ! common.geo
  21 !      common /geo/
  22 !-----------------------------------------------------------------------------
  23 ! common.locmove
  24 !     Variables (set in init routine) never modified by local_move
  25 !      common /loc_const/
  26       integer :: init_called
  27       logical :: locmove_output
  28       real(kind=8) :: min_theta, max_theta
  29       real(kind=8) :: dmin2,dmax2
  30       real(kind=8) :: flag,small,small2
  31 !     Workspace for local_move
  32 !      common /loc_work/
  33       integer :: a_n,b_n,res_n
  34       real(kind=8),dimension(0:7) :: a_ang
  35       real(kind=8),dimension(0:3) :: b_ang
  36       real(kind=8),dimension(0:11) :: res_ang
  37       logical,dimension(0:2,0:7) :: a_tab
  38       logical,dimension(0:2,0:3) :: b_tab
  39       logical,dimension(0:2,0:2,0:11) :: res_tab
  40 !-----------------------------------------------------------------------------
  41 !      integer,dimension(:),allocatable :: itype_pdb !(maxres) initialize in molread
  42 !-----------------------------------------------------------------------------
  43 !
  44 !
  45 !-----------------------------------------------------------------------------
  46       contains
  47 !-----------------------------------------------------------------------------
  48 ! arcos.f
  49 !-----------------------------------------------------------------------------
  50       real(kind=8) function ARCOS(X)
  51 !      implicit real*8 (a-h,o-z)
  52 !      include 'COMMON.GEO'
  53 !el local variables
  54       real(kind=8) :: x
  55       IF (DABS(X).LT.1.0D0) GOTO 1
  56       ARCOS=PIPOL*(1.0d0-DSIGN(1.0D0,X))
  57       RETURN
  58     1 ARCOS=DACOS(X)
  59       return
  60       end function ARCOS
  61 !-----------------------------------------------------------------------------
  62 ! chainbuild.F
  63 !-----------------------------------------------------------------------------
  64       subroutine chainbuild
  65 !
  66 ! Build the virtual polypeptide chain. Side-chain centroids are moveable.
  67 ! As of 2/17/95.
  68 !
  69 !      implicit real*8 (a-h,o-z)
  70 !      include 'DIMENSIONS'
  71 !      include 'COMMON.CHAIN'
  72 !      include 'COMMON.LOCAL'
  73 !      include 'COMMON.GEO'
  74 !      include 'COMMON.VAR'
  75 !      include 'COMMON.IOUNITS'
  76 !      include 'COMMON.NAMES'
  77 !      include 'COMMON.INTERACT'
  78       logical :: lprn
  79 !el local variables
  80       integer :: i,j
  81       real(kind=8) :: be,be1,alfai
  82       integer :: nres2
  83       nres2=2*nres
  84 ! Set lprn=.true. for debugging
  85       lprn = .false.
  86       print *,"I ENTER CHAINBUILD"
  87 !
  88 ! Define the origin and orientation of the coordinate system and locate the
  89 ! first three CA's and SC(2).
  90 !
  91 !elwrite(iout,*)"in chainbuild"
  92       call orig_frame
  93 !elwrite(iout,*)"after orig_frame"
  94 !
  95 ! Build the alpha-carbon chain.
  96 !
  97       do i=4,nres
  98         call locate_next_res(i)
  99       enddo
 100 !elwrite(iout,*)"after locate_next_res"
 101 !
 102 ! First and last SC must coincide with the corresponding CA.
 103 !
 104       do j=1,3
 105         dc(j,nres+1)=0.0D0
 106         dc_norm(j,nres+1)=0.0D0
 107         dc(j,nres+nres)=0.0D0
 108         dc_norm(j,nres+nres)=0.0D0
 109         c(j,nres+1)=c(j,1)
 110         c(j,nres+nres)=c(j,nres)
 111       enddo
 112 !
 113 ! Temporary diagnosis
 114 !
 115       if (lprn) then
 116
 117       call cartprint
 118       write (iout,'(/a)') 'Recalculated internal coordinates'
 119       do i=2,nres-1
 120         do j=1,3
 121           c(j,nres2+2)=0.5D0*(c(j,i-1)+c(j,i+1))        !maxres2=2*maxres
 122         enddo
 123         be=0.0D0
 124         if (i.gt.3) be=rad2deg*beta(i-3,i-2,i-1,i)
 125         be1=rad2deg*beta(nres+i,i,nres2+2,i+1)
 126         alfai=0.0D0
 127         if (i.gt.2) alfai=rad2deg*alpha(i-2,i-1,i)
 128         write (iout,1212) restyp(itype(i,1),1),i,dist(i-1,i),&
 129         alfai,be,dist(nres+i,i),rad2deg*alpha(nres+i,i,nres2+2),be1
 130       enddo
 131  1212 format (a3,'(',i3,')',2(f10.5,2f10.2))
 132
 133       endif
 134
 135       return
 136       end subroutine chainbuild
 137 !-----------------------------------------------------------------------------
 138       subroutine orig_frame
 139 !
 140 ! Define the origin and orientation of the coordinate system and locate
 141 ! the first three atoms.
 142 !
 143 !      implicit real*8 (a-h,o-z)
 144 !      include 'DIMENSIONS'
 145 !      include 'COMMON.CHAIN'
 146 !      include 'COMMON.LOCAL'
 147 !      include 'COMMON.GEO'
 148 !      include 'COMMON.VAR'
 149 !el local variables
 150       integer :: i,j
 151       real(kind=8) :: cost,sint
 152
 153 !el      allocate(t(3,3,nres))  !(3,3,maxres)
 154 !el      allocate(r(3,3,nres))  !(3,3,maxres)
 155 !el      allocate(rt(3,3,nres)) !(3,3,maxres)
 156 !el      allocate(dc_norm(3,0:2*nres))  !(3,0:maxres2)
 157 !el      allocate(prod(3,3,nres))       !(3,3,maxres)
 158
 159       cost=dcos(theta(3))
 160       sint=dsin(theta(3))
 161       t(1,1,1)=-cost
 162       t(1,2,1)=-sint
 163       t(1,3,1)= 0.0D0
 164       t(2,1,1)=-sint
 165       t(2,2,1)= cost
 166       t(2,3,1)= 0.0D0
 167       t(3,1,1)= 0.0D0
 168       t(3,2,1)= 0.0D0
 169       t(3,3,1)= 1.0D0
 170       r(1,1,1)= 1.0D0
 171       r(1,2,1)= 0.0D0
 172       r(1,3,1)= 0.0D0
 173       r(2,1,1)= 0.0D0
 174       r(2,2,1)= 1.0D0
 175       r(2,3,1)= 0.0D0
 176       r(3,1,1)= 0.0D0
 177       r(3,2,1)= 0.0D0
 178       r(3,3,1)= 1.0D0
 179       do i=1,3
 180         do j=1,3
 181           rt(i,j,1)=t(i,j,1)
 182         enddo
 183       enddo
 184       do i=1,3
 185         do j=1,3
 186           prod(i,j,1)=0.0D0
 187           prod(i,j,2)=t(i,j,1)
 188         enddo
 189         prod(i,i,1)=1.0D0
 190       enddo
 191       c(1,1)=0.0D0
 192       c(2,1)=0.0D0
 193       c(3,1)=0.0D0
 194       c(1,2)=vbld(2)
 195       c(2,2)=0.0D0
 196       c(3,2)=0.0D0
 197       dc(1,0)=0.0d0
 198       dc(2,0)=0.0D0
 199       dc(3,0)=0.0D0
 200       dc(1,1)=vbld(2)
 201       dc(2,1)=0.0D0
 202       dc(3,1)=0.0D0
 203       dc_norm(1,0)=0.0D0
 204       dc_norm(2,0)=0.0D0
 205       dc_norm(3,0)=0.0D0
 206       dc_norm(1,1)=1.0D0
 207       dc_norm(2,1)=0.0D0
 208       dc_norm(3,1)=0.0D0
 209       do j=1,3
 210         dc_norm(j,2)=prod(j,1,2)
 211         dc(j,2)=vbld(3)*prod(j,1,2)
 212         c(j,3)=c(j,2)+dc(j,2)
 213       enddo
 214       call locate_side_chain(2)
 215       return
 216       end subroutine orig_frame
 217 !-----------------------------------------------------------------------------
 218       subroutine locate_next_res(i)
 219 !
 220 ! Locate CA(i) and SC(i-1)
 221 !
 222 !      implicit real*8 (a-h,o-z)
 223 !      include 'DIMENSIONS'
 224 !      include 'COMMON.CHAIN'
 225 !      include 'COMMON.LOCAL'
 226 !      include 'COMMON.GEO'
 227 !      include 'COMMON.VAR'
 228 !      include 'COMMON.IOUNITS'
 229 !      include 'COMMON.NAMES'
 230 !      include 'COMMON.INTERACT'
 231 !
 232 ! Define the rotation matrices corresponding to CA(i)
 233 !
 234 !el local variables
 235       integer :: i,j
 236       real(kind=8) :: theti,phii
 237       real(kind=8) :: cost,sint,cosphi,sinphi
 238 #ifdef OSF
 239 #ifdef WHAM_RUN
 240       theti=theta(i)
 241       icrc=0
 242       call proc_proc(theti,icrc)
 243       if(icrc.eq.1)theti=100.0
 244       phii=phi(i)
 245       icrc=0
 246       call proc_proc(phii,icrc)
 247       if(icrc.eq.1)phii=180.0
 248 #else
 249       theti=theta(i)
 250       if (theti.ne.theti) theti=100.0
 251       phii=phi(i)
 252       if (phii.ne.phii) phii=180.0
 253 #endif
 254 #else
 255       theti=theta(i)
 256       phii=phi(i)
 257 #endif
 258       cost=dcos(theti)
 259       sint=dsin(theti)
 260       cosphi=dcos(phii)
 261       sinphi=dsin(phii)
 262 ! Define the matrices of the rotation about the virtual-bond valence angles
 263 ! theta, T(i,j,k), virtual-bond dihedral angles gamma (miscalled PHI in this
 264 ! program), R(i,j,k), and, the cumulative matrices of rotation RT
 265       t(1,1,i-2)=-cost
 266       t(1,2,i-2)=-sint
 267       t(1,3,i-2)= 0.0D0
 268       t(2,1,i-2)=-sint
 269       t(2,2,i-2)= cost
 270       t(2,3,i-2)= 0.0D0
 271       t(3,1,i-2)= 0.0D0
 272       t(3,2,i-2)= 0.0D0
 273       t(3,3,i-2)= 1.0D0
 274       r(1,1,i-2)= 1.0D0
 275       r(1,2,i-2)= 0.0D0
 276       r(1,3,i-2)= 0.0D0
 277       r(2,1,i-2)= 0.0D0
 278       r(2,2,i-2)=-cosphi
 279       r(2,3,i-2)= sinphi
 280       r(3,1,i-2)= 0.0D0
 281       r(3,2,i-2)= sinphi
 282       r(3,3,i-2)= cosphi
 283       rt(1,1,i-2)=-cost
 284       rt(1,2,i-2)=-sint
 285       rt(1,3,i-2)=0.0D0
 286       rt(2,1,i-2)=sint*cosphi
 287       rt(2,2,i-2)=-cost*cosphi
 288       rt(2,3,i-2)=sinphi
 289       rt(3,1,i-2)=-sint*sinphi
 290       rt(3,2,i-2)=cost*sinphi
 291       rt(3,3,i-2)=cosphi
 292       call matmult(prod(1,1,i-2),rt(1,1,i-2),prod(1,1,i-1))
 293       do j=1,3
 294         dc_norm(j,i-1)=prod(j,1,i-1)
 295         dc(j,i-1)=vbld(i)*prod(j,1,i-1)
 296         c(j,i)=c(j,i-1)+dc(j,i-1)
 297       enddo
 298 !d    print '(2i3,2(3f10.5,5x))', i-1,i,(dc(j,i-1),j=1,3),(c(j,i),j=1,3)
 299 !
 300 ! Now calculate the coordinates of SC(i-1)
 301 !
 302       call locate_side_chain(i-1)
 303       return
 304       end subroutine locate_next_res
 305 !-----------------------------------------------------------------------------
 306       subroutine locate_side_chain(i)
 307 !
 308 ! Locate the side-chain centroid i, 1 < i < NRES. Put in C(*,NRES+i).
 309 !
 310 !      implicit real*8 (a-h,o-z)
 311 !      include 'DIMENSIONS'
 312 !      include 'COMMON.CHAIN'
 313 !      include 'COMMON.LOCAL'
 314 !      include 'COMMON.GEO'
 315 !      include 'COMMON.VAR'
 316 !      include 'COMMON.IOUNITS'
 317 !      include 'COMMON.NAMES'
 318 !      include 'COMMON.INTERACT'
 319       integer :: i,j,k
 320       real(kind=8),dimension(3) :: xx
 321       real(kind=8) :: alphi,omegi,theta2
 322       real(kind=8) :: dsci,dsci_inv,sinalphi,cosalphi,cosomegi,sinomegi
 323       real(kind=8) :: xp,yp,zp,cost2,sint2,rj
 324 !      dsci=dsc(itype(i,1))
 325 !      dsci_inv=dsc_inv(itype(i,1))
 326       dsci=vbld(i+nres)
 327       dsci_inv=vbld_inv(i+nres)
 328 #ifdef OSF
 329       alphi=alph(i)
 330       omegi=omeg(i)
 331 #ifdef WHAM_RUN
 332 ! detecting NaNQ
 333       icrc=0
 334       call proc_proc(alphi,icrc)
 335       if(icrc.eq.1)alphi=100.0
 336       icrc=0
 337       call proc_proc(omegi,icrc)
 338       if(icrc.eq.1)omegi=-100.0
 339 #else
 340       if (alphi.ne.alphi) alphi=100.0
 341       if (omegi.ne.omegi) omegi=-100.0
 342 #endif
 343 #else
 344       alphi=alph(i)
 345       omegi=omeg(i)
 346 #endif
 347       cosalphi=dcos(alphi)
 348       sinalphi=dsin(alphi)
 349       cosomegi=dcos(omegi)
 350       sinomegi=dsin(omegi)
 351       xp= dsci*cosalphi
 352       yp= dsci*sinalphi*cosomegi
 353       zp=-dsci*sinalphi*sinomegi
 354 ! Now we have to rotate the coordinate system by 180-theta(i)/2 so as to get its
 355 ! X-axis aligned with the vector DC(*,i)
 356       theta2=pi-0.5D0*theta(i+1)
 357       cost2=dcos(theta2)
 358       sint2=dsin(theta2)
 359       xx(1)= xp*cost2+yp*sint2
 360       xx(2)=-xp*sint2+yp*cost2
 361       xx(3)= zp
 362 !d    print '(a3,i3,3f10.5,5x,3f10.5)',restyp(itype(i,1)),i,
 363 !d   &   xp,yp,zp,(xx(k),k=1,3)
 364       do j=1,3
 365         xloc(j,i)=xx(j)
 366       enddo
 367 ! Bring the SC vectors to the common coordinate system.
 368       xx(1)=xloc(1,i)
 369       xx(2)=xloc(2,i)*r(2,2,i-1)+xloc(3,i)*r(2,3,i-1)
 370       xx(3)=xloc(2,i)*r(3,2,i-1)+xloc(3,i)*r(3,3,i-1)
 371       do j=1,3
 372         xrot(j,i)=xx(j)
 373       enddo
 374       do j=1,3
 375         rj=0.0D0
 376         do k=1,3
 377           rj=rj+prod(j,k,i-1)*xx(k)
 378         enddo
 379         dc(j,nres+i)=rj
 380         dc_norm(j,nres+i)=rj*dsci_inv
 381         c(j,nres+i)=c(j,i)+rj
 382       enddo
 383       return
 384       end subroutine locate_side_chain
 385 !-----------------------------------------------------------------------------
 386 ! checkder_p.F
 387 !-----------------------------------------------------------------------------
 388       subroutine int_from_cart1(lprn)
 389 !      implicit real*8 (a-h,o-z)
 390 !      include 'DIMENSIONS'
 391 #ifdef MPI
 392       include 'mpif.h'
 393       integer :: ierror
 394 #endif
 395 !      include 'COMMON.IOUNITS'
 396 !      include 'COMMON.VAR'
 397 !      include 'COMMON.CHAIN'
 398 !      include 'COMMON.GEO'
 399 !      include 'COMMON.INTERACT'
 400 !      include 'COMMON.LOCAL'
 401 !      include 'COMMON.NAMES'
 402 !      include 'COMMON.SETUP'
 403 !      include 'COMMON.TIME1'
 404       logical :: lprn
 405 !el local variables
 406       integer :: i,j
 407       real(kind=8) :: dnorm1,dnorm2,be
 408       integer :: nres2
 409       nres2=2*nres
 410       if (lprn) write (iout,'(/a)') 'Recalculated internal coordinates'
 411 #ifdef TIMING
 412       time01=MPI_Wtime()
 413 #endif
 414
 415 #ifdef WHAM_RUN
 416       vbld(nres+1)=0.0d0
 417 !write(iout,*)"geometry warring, vbld=",(vbld(i),i=1,nres+1)
 418       vbld(2*nres)=0.0d0
 419       vbld_inv(nres+1)=0.0d0
 420       vbld_inv(2*nres)=0.0d0
 421 #endif
 422
 423 #if defined(PARINT) && defined(MPI)
 424       do i=iint_start,iint_end
 425 #else
 426       do i=2,nres
 427 #endif
 428         dnorm1=dist(i-1,i)
 429         dnorm2=dist(i,i+1)
 430         do j=1,3
 431           c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))/dnorm1 &
 432            +(c(j,i+1)-c(j,i))/dnorm2)
 433         enddo
 434         be=0.0D0
 435         if (i.gt.2) then
 436         if (i.le.nres) phi(i+1)=beta(i-2,i-1,i,i+1)
 437         if ((itype(i,1).ne.10).and.(itype(i-1,1).ne.10)) then
 438          tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
 439         endif
 440         if (itype(i-1,1).ne.10) then
 441          tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
 442          omicron(1,i)=alpha(i-2,i-1,i-1+nres)
 443          omicron(2,i)=alpha(i-1+nres,i-1,i)
 444         endif
 445         if (itype(i,1).ne.10) then
 446          tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
 447         endif
 448         endif
 449         omeg(i)=beta(nres+i,i,nres2+2,i+1)
 450         alph(i)=alpha(nres+i,i,nres2+2)
 451         theta(i+1)=alpha(i-1,i,i+1)
 452         vbld(i)=dist(i-1,i)
 453 !        print *,i,vbld(i),"vbld(i)"
 454         vbld_inv(i)=1.0d0/vbld(i)
 455         vbld(nres+i)=dist(nres+i,i)
 456         if (itype(i,1).ne.10) then
 457           vbld_inv(nres+i)=1.0d0/vbld(nres+i)
 458         else
 459           vbld_inv(nres+i)=0.0d0
 460         endif
 461       enddo
 462 #if defined(PARINT) && defined(MPI)
 463        if (nfgtasks1.gt.1) then
 464 !d       write(iout,*) "iint_start",iint_start," iint_count",
 465 !d     &   (iint_count(i),i=0,nfgtasks-1)," iint_displ",
 466 !d     &   (iint_displ(i),i=0,nfgtasks-1)
 467 !d       write (iout,*) "Gather vbld backbone"
 468 !d       call flush(iout)
 469        time00=MPI_Wtime()
 470        call MPI_Allgatherv(vbld(iint_start),iint_count(fg_rank1),&
 471          MPI_DOUBLE_PRECISION,vbld(1),iint_count(0),iint_displ(0),&
 472          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 473 !d       write (iout,*) "Gather vbld_inv"
 474 !d       call flush(iout)
 475        call MPI_Allgatherv(vbld_inv(iint_start),iint_count(fg_rank1),&
 476          MPI_DOUBLE_PRECISION,vbld_inv(1),iint_count(0),iint_displ(0),&
 477          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 478 !d       write (iout,*) "Gather vbld side chain"
 479 !d       call flush(iout)
 480        call MPI_Allgatherv(vbld(iint_start+nres),iint_count(fg_rank1),&
 481          MPI_DOUBLE_PRECISION,vbld(nres+1),iint_count(0),iint_displ(0),&
 482          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 483 !d       write (iout,*) "Gather vbld_inv side chain"
 484 !d       call flush(iout)
 485        call MPI_Allgatherv(vbld_inv(iint_start+nres),&
 486          iint_count(fg_rank1),MPI_DOUBLE_PRECISION,vbld_inv(nres+1),&
 487          iint_count(0),iint_displ(0),MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 488 !d       write (iout,*) "Gather theta"
 489 !d       call flush(iout)
 490        call MPI_Allgatherv(theta(iint_start+1),iint_count(fg_rank1),&
 491          MPI_DOUBLE_PRECISION,theta(2),iint_count(0),iint_displ(0),&
 492          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 493 !d       write (iout,*) "Gather phi"
 494 !d       call flush(iout)
 495        call MPI_Allgatherv(phi(iint_start+1),iint_count(fg_rank1),&
 496          MPI_DOUBLE_PRECISION,phi(2),iint_count(0),iint_displ(0),&
 497          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 498 #ifdef CRYST_SC
 499 !d       write (iout,*) "Gather alph"
 500 !d       call flush(iout)
 501        call MPI_Allgatherv(alph(iint_start),iint_count(fg_rank1),&
 502          MPI_DOUBLE_PRECISION,alph(1),iint_count(0),iint_displ(0),&
 503          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 504 !d       write (iout,*) "Gather omeg"
 505 !d       call flush(iout)
 506        call MPI_Allgatherv(omeg(iint_start),iint_count(fg_rank1),&
 507          MPI_DOUBLE_PRECISION,omeg(1),iint_count(0),iint_displ(0),&
 508          MPI_DOUBLE_PRECISION,FG_COMM1,IERR)
 509 #endif
 510        time_gather=time_gather+MPI_Wtime()-time00
 511       endif
 512 #endif
 513       do i=1,nres-1
 514         do j=1,3
 515 !#ifdef WHAM_RUN
 516 #if defined(WHAM_RUN) || defined(CLUSTER)
 517           dc(j,i)=c(j,i+1)-c(j,i)
 518 #endif
 519           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
 520         enddo
 521       enddo
 522       do i=2,nres-1
 523         do j=1,3
 524 !#ifdef WHAM_RUN
 525 #if defined(WHAM_RUN) || defined(CLUSTER)
 526           dc(j,i+nres)=c(j,i+nres)-c(j,i)
 527 #endif
 528           dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
 529         enddo
 530       enddo
 531       if (lprn) then
 532       do i=2,nres
 533        write (iout,1212) restyp(itype(i,1),1),i,vbld(i),&
 534        rad2deg*theta(i),rad2deg*phi(i),vbld(nres+i),&
 535        rad2deg*alph(i),rad2deg*omeg(i)
 536       enddo
 537       endif
 538  1212 format (a3,'(',i3,')',2(f15.10,2f10.2))
 539 #ifdef TIMING
 540       time_intfcart=time_intfcart+MPI_Wtime()-time01
 541 #endif
 542       return
 543       end subroutine int_from_cart1
 544 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 545 !-----------------------------------------------------------------------------
 546 ! check_sc_distr.f
 547 !-----------------------------------------------------------------------------
 548       subroutine check_sc_distr
 549 !      implicit real*8 (a-h,o-z)
 550 !      include 'DIMENSIONS'
 551 !      include 'COMMON.TIME1'
 552 !      include 'COMMON.INTERACT'
 553 !      include 'COMMON.NAMES'
 554 !      include 'COMMON.GEO'
 555 !      include 'COMMON.HEADER'
 556 !      include 'COMMON.CONTROL'
 557       logical :: fail
 558       real(kind=8),dimension(6*nres) :: varia !(maxvar) (maxvar=6*maxres)
 559       real(kind=8) :: hrtime,mintime,sectime
 560       integer,parameter :: MaxSample=10000000
 561       real(kind=8),parameter :: delt=1.0D0/MaxSample
 562       real(kind=8),dimension(0:72,0:90) :: prob
 563 !el local variables
 564       integer :: it,i,j,isample,indal,indom
 565       real(kind=8) :: al,om,dV
 566       dV=2.0D0*5.0D0*deg2rad*deg2rad
 567       print *,'dv=',dv
 568       do 10 it=1,1
 569         if ((it.eq.10).or.(it.eq.ntyp1)) goto 10
 570         open (20,file=restyp(it,1)//'_distr.sdc',status='unknown')
 571         call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
 572         close (20)
 573         goto 10
 574         open (20,file=restyp(it,1)//'_distr1.sdc',status='unknown')
 575         do i=0,90
 576           do j=0,72
 577             prob(j,i)=0.0D0
 578           enddo
 579         enddo
 580         do isample=1,MaxSample
 581           call gen_side(it,90.0D0 * deg2rad,al,om,fail,1)
 582           indal=rad2deg*al/2
 583           indom=(rad2deg*om+180.0D0)/5
 584           prob(indom,indal)=prob(indom,indal)+delt
 585         enddo
 586         do i=45,90
 587           do j=0,72
 588             write (20,'(2f10.3,1pd15.5)') 2*i+0.0D0,5*j-180.0D0,&
 589                     prob(j,i)/dV
 590           enddo
 591         enddo
 592    10   continue
 593       return
 594       end subroutine check_sc_distr
 595 #endif
 596 !-----------------------------------------------------------------------------
 597 ! convert.f
 598 !-----------------------------------------------------------------------------
 599       subroutine geom_to_var(n,x)
 600 !
 601 ! Transfer the geometry parameters to the variable array.
 602 ! The positions of variables are as follows:
 603 ! 1. Virtual-bond torsional angles: 1 thru nres-3
 604 ! 2. Virtual-bond valence angles: nres-2 thru 2*nres-5
 605 ! 3. The polar angles alpha of local SC orientation: 2*nres-4 thru
 606 !    2*nres-4+nside
 607 ! 4. The torsional angles omega of SC orientation: 2*nres-4+nside+1
 608 !    thru 2*nre-4+2*nside
 609 !
 610 !      implicit real*8 (a-h,o-z)
 611 !      include 'DIMENSIONS'
 612 !      include 'COMMON.VAR'
 613 !      include 'COMMON.GEO'
 614 !      include 'COMMON.CHAIN'
 615       integer :: n,i
 616       real(kind=8),dimension(n) :: x
 617 !d    print *,'nres',nres,' nphi',nphi,' ntheta',ntheta,' nvar',nvar
 618       do i=4,nres
 619         x(i-3)=phi(i)
 620 !d      print *,i,i-3,phi(i)
 621       enddo
 622       if (n.eq.nphi) return
 623       do i=3,nres
 624         x(i-2+nphi)=theta(i)
 625 !d      print *,i,i-2+nphi,theta(i)
 626       enddo
 627       if (n.eq.nphi+ntheta) return
 628       do i=2,nres-1
 629         if (ialph(i,1).gt.0) then
 630           x(ialph(i,1))=alph(i)
 631           x(ialph(i,1)+nside)=omeg(i)
 632 !d        print *,i,ialph(i,1),ialph(i,1)+nside,alph(i),omeg(i)
 633         endif
 634       enddo
 635       return
 636       end subroutine geom_to_var
 637 !-----------------------------------------------------------------------------
 638       subroutine var_to_geom(n,x)
 639 !
 640 ! Update geometry parameters according to the variable array.
 641 !
 642 !      implicit real*8 (a-h,o-z)
 643 !      include 'DIMENSIONS'
 644 !      include 'COMMON.VAR'
 645 !      include 'COMMON.CHAIN'
 646 !      include 'COMMON.GEO'
 647 !      include 'COMMON.IOUNITS'
 648       integer :: n,i,ii
 649       real(kind=8),dimension(n) :: x
 650       logical :: change !,reduce
 651 !el      alph=0.0d0
 652 !el      omeg=0.0d0
 653 !el      phi=0.0d0
 654 !el      theta=0.0d0
 655
 656       change=reduce(x)
 657       if (n.gt.nphi+ntheta) then
 658         do i=1,nside
 659           ii=ialph(i,2)
 660           alph(ii)=x(nphi+ntheta+i)
 661           omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
 662 !elwrite(iout,*) "alph",ii,alph
 663 !elwrite(iout,*) "omeg",ii,omeg
 664         enddo
 665       endif
 666       do i=4,nres
 667         phi(i)=x(i-3)
 668 !elwrite(iout,*) "phi",i,phi
 669       enddo
 670       if (n.eq.nphi) return
 671       do i=3,nres
 672         theta(i)=x(i-2+nphi)
 673 !elwrite(iout,*) "theta",i,theta
 674         if (theta(i).eq.pi) theta(i)=0.99d0*pi
 675         x(i-2+nphi)=theta(i)
 676       enddo
 677       return
 678       end subroutine var_to_geom
 679 !-----------------------------------------------------------------------------
 680       logical function convert_side(alphi,omegi)
 681 !      implicit none
 682       real(kind=8) :: alphi,omegi
 683 !el      real(kind=8) :: pinorm
 684 !      include 'COMMON.GEO'
 685       convert_side=.false.
 686 ! Apply periodicity restrictions.
 687       if (alphi.gt.pi) then
 688         alphi=dwapi-alphi
 689         omegi=pinorm(omegi+pi)
 690         convert_side=.true.
 691       endif
 692       return
 693       end function convert_side
 694 !-----------------------------------------------------------------------------
 695       logical function reduce(x)
 696 !
 697 ! Apply periodic restrictions to variables.
 698 !
 699 !      implicit real*8 (a-h,o-z)
 700 !      include 'DIMENSIONS'
 701 !      include 'COMMON.VAR'
 702 !      include 'COMMON.CHAIN'
 703 !      include 'COMMON.GEO'
 704       logical :: zm,zmiana      !,convert_side
 705       real(kind=8),dimension(nvar) :: x
 706       integer :: i,ii,iii
 707       zmiana=.false.
 708       do i=4,nres
 709         x(i-3)=pinorm(x(i-3))
 710       enddo
 711       if (nvar.gt.nphi+ntheta) then
 712         do i=1,nside
 713           ii=nphi+ntheta+i
 714           iii=ii+nside
 715           x(ii)=thetnorm(x(ii))
 716           x(iii)=pinorm(x(iii))
 717 ! Apply periodic restrictions.
 718           zm=convert_side(x(ii),x(iii))
 719           zmiana=zmiana.or.zm
 720         enddo
 721       endif
 722       if (nvar.eq.nphi) return
 723       do i=3,nres
 724         ii=i-2+nphi
 725         iii=i-3
 726         x(ii)=dmod(x(ii),dwapi)
 727 ! Apply periodic restrictions.
 728         if (x(ii).gt.pi) then
 729           zmiana=.true.
 730           x(ii)=dwapi-x(ii)
 731           if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
 732           if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
 733           ii=ialph(i-1,1)
 734           if (ii.gt.0) then
 735             x(ii)=dmod(pi-x(ii),dwapi)
 736             x(ii+nside)=pinorm(-x(ii+nside))
 737             zm=convert_side(x(ii),x(ii+nside))
 738           endif
 739         else if (x(ii).lt.-pi) then
 740           zmiana=.true.
 741           x(ii)=dwapi+x(ii)
 742           ii=ialph(i-1,1)
 743           if (ii.gt.0) then
 744             x(ii)=dmod(pi-x(ii),dwapi)
 745             x(ii+nside)=pinorm(-pi-x(ii+nside))
 746             zm=convert_side(x(ii),x(ii+nside))
 747           endif
 748         else if (x(ii).lt.0.0d0) then
 749           zmiana=.true.
 750           x(ii)=-x(ii)
 751           if (iii.gt.0) x(iii)=pinorm(x(iii)+pi)
 752           if (i.lt.nres) x(iii+1)=pinorm(x(iii+1)+pi)
 753           ii=ialph(i-1,1)
 754           if (ii.gt.0) then
 755             x(ii+nside)=pinorm(-x(ii+nside))
 756             zm=convert_side(x(ii),x(ii+nside))
 757           endif
 758         endif
 759       enddo
 760       reduce=zmiana
 761       return
 762       end function reduce
 763 !-----------------------------------------------------------------------------
 764       real(kind=8) function thetnorm(x)
 765 ! This function puts x within [0,2Pi].
 766       implicit none
 767       real(kind=8) :: x,xx
 768 !      include 'COMMON.GEO'
 769       xx=dmod(x,dwapi)
 770       if (xx.lt.0.0d0) xx=xx+dwapi
 771       if (xx.gt.0.9999d0*pi) xx=0.9999d0*pi
 772       thetnorm=xx
 773       return
 774       end function thetnorm
 775 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
 776 !-----------------------------------------------------------------------------
 777       subroutine var_to_geom_restr(n,xx)
 778 !
 779 ! Update geometry parameters according to the variable array.
 780 !
 781 !      implicit real*8 (a-h,o-z)
 782 !      include 'DIMENSIONS'
 783 !      include 'COMMON.VAR'
 784 !      include 'COMMON.CHAIN'
 785 !      include 'COMMON.GEO'
 786 !      include 'COMMON.IOUNITS'
 787       integer :: n,i,ii
 788       real(kind=8),dimension(6*nres) :: x,xx !(maxvar) (maxvar=6*maxres)
 789       logical :: change !,reduce
 790
 791       call xx2x(x,xx)
 792       change=reduce(x)
 793       do i=1,nside
 794           ii=ialph(i,2)
 795           alph(ii)=x(nphi+ntheta+i)
 796           omeg(ii)=pinorm(x(nphi+ntheta+nside+i))
 797       enddo
 798       do i=4,nres
 799         phi(i)=x(i-3)
 800       enddo
 801       do i=3,nres
 802         theta(i)=x(i-2+nphi)
 803         if (theta(i).eq.pi) theta(i)=0.99d0*pi
 804         x(i-2+nphi)=theta(i)
 805       enddo
 806       return
 807       end subroutine var_to_geom_restr
 808 !-----------------------------------------------------------------------------
 809 ! gen_rand_conf.F
 810 !-----------------------------------------------------------------------------
 811       subroutine gen_rand_conf(nstart,*)
 812 ! Generate random conformation or chain cut and regrowth.
 813       use mcm_data
 814       use random, only: iran_num,ran_number
 815 !      implicit real*8 (a-h,o-z)
 816 !      include 'DIMENSIONS'
 817 !      include 'COMMON.CHAIN'
 818 !      include 'COMMON.LOCAL'
 819 !      include 'COMMON.VAR'
 820 !      include 'COMMON.INTERACT'
 821 !      include 'COMMON.IOUNITS'
 822 !      include 'COMMON.MCM'
 823 !      include 'COMMON.GEO'
 824 !      include 'COMMON.CONTROL'
 825       logical :: back,fail      !overlap,
 826 !el local variables
 827       integer :: i,nstart,maxsi,nsi,maxnit,nit,niter
 828       integer :: it1,it2,it,j
 829 !d    print *,' CG Processor',me,' maxgen=',maxgen
 830       maxsi=1000
 831 !      write (iout,*) 'Gen_Rand_conf: nstart=',nstart
 832       if (nstart.lt.5) then
 833         it1=iabs(itype(2,1))
 834         phi(4)=gen_phi(4,iabs(itype(2,1)),iabs(itype(3,1)))
 835 !       write(iout,*)'phi(4)=',rad2deg*phi(4)
 836         if (nstart.lt.3) theta(3)=gen_theta(iabs(itype(2,1)),pi,phi(4),molnum(2))
 837 !       write(iout,*)'theta(3)=',rad2deg*theta(3)
 838         if ((it1.ne.10).and.(it1.ne.ntyp1)) then
 839           nsi=0
 840           fail=.true.
 841           do while (fail.and.nsi.le.maxsi)
 842             call gen_side(it1,theta(3),alph(2),omeg(2),fail,molnum(2))
 843             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),molnum(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,molnum(i-2))
 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),molnum(i))
 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,molnum(i))
 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,mnum)
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,mnum
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 if (mnum.eq.1) then
1077
1078       thet_pred_mean=a0thet(it)
1079 !      write(iout,*),it,thet_pred_mean,"gen_thet"
1080       do k=1,2
1081         thet_pred_mean=thet_pred_mean+athet(k,it,1,1)*y(k) &
1082            +bthet(k,it,1,1)*z(k)
1083       enddo
1084       sig=polthet(3,it)
1085       do j=2,0,-1
1086         sig=sig*thet_pred_mean+polthet(j,it)
1087       enddo
1088       sig=0.5D0/(sig*sig+sigc0(it))
1089       ak=dexp(gthet(1,it)- &
1090        0.5D0*((gthet(2,it)-thet_pred_mean)/gthet(3,it))**2)
1091 !     print '(i5,5(1pe14.4))',it,(gthet(j,it),j=1,3)
1092 !     print '(5(1pe14.4))',thet_pred_mean,theta0(it),sig,sig0(it),ak
1093       theta_temp=binorm(thet_pred_mean,theta0(it),sig,sig0(it),ak)
1094       if (theta_temp.lt.theta_min) theta_temp=theta_min
1095       if (theta_temp.gt.theta_max) theta_temp=theta_max
1096       gen_theta=theta_temp
1097 !     print '(a)','Exiting GENTHETA.'
1098       else if (mnum.eq.2) then
1099        gen_theta=aa0thet_nucl(1,it,1) -0.17 + ran_number(0.0d0,0.34d0)
1100       else
1101               gen_theta=ran_number(theta_max/2.0,theta_max)
1102        endif
1103       return
1104       end function gen_theta
1105 !-----------------------------------------------------------------------------
1106       subroutine gen_side(it,the,al,om,fail,mnum)
1107       use random, only:ran_number,mult_norm1
1108 !      implicit real*8 (a-h,o-z)
1109 !      include 'DIMENSIONS'
1110 !      include 'COMMON.GEO'
1111 !      include 'COMMON.LOCAL'
1112 !      include 'COMMON.SETUP'
1113 !      include 'COMMON.IOUNITS'
1114       real(kind=8) :: MaxBoxLen=10.0D0
1115       real(kind=8),dimension(3,3) :: Ap_inv,a,vec
1116       real(kind=8),dimension(:,:),allocatable :: z !(3,maxlob)
1117       real(kind=8),dimension(:),allocatable :: W1,detAp !(maxlob)
1118       real(kind=8),dimension(:),allocatable :: sumW !(0:maxlob)
1119       real(kind=8),dimension(2) :: y,cm,eig
1120       real(kind=8),dimension(2,2) :: box
1121       real(kind=8),dimension(100) :: work
1122       real(kind=8) :: eig_limit=1.0D-8
1123       real(kind=8) :: Big=10.0D0
1124       logical :: lprint,fail,lcheck
1125 !el local variables
1126       integer :: it,i,j,k,l,nlobit,ial,iom,iii,ilob,mnum
1127       real(kind=8) :: the,al,om,detApi,wart,y2,wykl,radmax
1128       real(kind=8) :: tant,zz1,W1i,radius,zk,fac,dV,sum,sum1
1129       real(kind=8) :: which_lobe
1130       lcheck=.false.
1131       lprint=.false.
1132       fail=.false.
1133       if (mnum.eq.1) then
1134       if (the.eq.0.0D0 .or. the.eq.pi) then
1135 #ifdef MPI
1136         write (*,'(a,i4,a,i3,a,1pe14.5)') &
1137        'CG Processor:',me,' Error in GenSide: it=',it,' theta=',the
1138 #else
1139 !d        write (iout,'(a,i3,a,1pe14.5)')
1140 !d     &   'Error in GenSide: it=',it,' theta=',the
1141 #endif
1142         fail=.true.
1143         return
1144       endif
1145       tant=dtan(the-pipol)
1146       nlobit=nlob(it)
1147       allocate(z(3,nlobit))
1148       allocate(W1(nlobit))
1149       allocate(detAp(nlobit))
1150       allocate(sumW(0:nlobit))
1151       if (lprint) then
1152 #ifdef MPI
1153         print '(a,i4,a)','CG Processor:',me,' Enter Gen_Side.'
1154         write (iout,'(a,i4,a)') 'Processor:',me,' Enter Gen_Side.'
1155 #endif
1156         print *,'it=',it,' nlobit=',nlobit,' the=',the,' tant=',tant
1157         write (iout,*) 'it=',it,' nlobit=',nlobit,' the=',the,&
1158            ' tant=',tant
1159       endif
1160       do i=1,nlobit
1161        zz1=tant-censc(1,i,it)
1162         do k=1,3
1163           do l=1,3
1164             a(k,l)=gaussc(k,l,i,it)
1165           enddo
1166         enddo
1167         detApi=a(2,2)*a(3,3)-a(2,3)**2
1168         Ap_inv(2,2)=a(3,3)/detApi
1169         Ap_inv(2,3)=-a(2,3)/detApi
1170         Ap_inv(3,2)=Ap_inv(2,3)
1171         Ap_inv(3,3)=a(2,2)/detApi
1172         if (lprint) then
1173           write (*,'(/a,i2/)') 'Cluster #',i
1174           write (*,'(3(1pe14.5),5x,1pe14.5)') &
1175           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1176           write (iout,'(/a,i2/)') 'Cluster #',i
1177           write (iout,'(3(1pe14.5),5x,1pe14.5)') &
1178           ((a(l,k),l=1,3),censc(k,i,it),k=1,3)
1179         endif
1180         W1i=0.0D0
1181         do k=2,3
1182           do l=2,3
1183             W1i=W1i+a(k,1)*a(l,1)*Ap_inv(k,l)
1184           enddo
1185         enddo
1186         W1i=a(1,1)-W1i
1187         W1(i)=dexp(bsc(i,it)-0.5D0*W1i*zz1*zz1)
1188 !        if (lprint) write(*,'(a,3(1pe15.5)/)')
1189 !     &          'detAp, W1, anormi',detApi,W1i,anormi
1190         do k=2,3
1191           zk=censc(k,i,it)
1192           do l=2,3
1193             zk=zk+zz1*Ap_inv(k,l)*a(l,1)
1194           enddo
1195           z(k,i)=zk
1196         enddo
1197         detAp(i)=dsqrt(detApi)
1198       enddo
1199
1200       if (lprint) then
1201         print *,'W1:',(w1(i),i=1,nlobit)
1202         print *,'detAp:',(detAp(i),i=1,nlobit)
1203         print *,'Z'
1204         do i=1,nlobit
1205           print '(i2,3f10.5)',i,(rad2deg*z(j,i),j=2,3)
1206         enddo
1207         write (iout,*) 'W1:',(w1(i),i=1,nlobit)
1208         write (iout,*) 'detAp:',(detAp(i),i=1,nlobit)
1209         write (iout,*) 'Z'
1210         do i=1,nlobit
1211           write (iout,'(i2,3f10.5)') i,(rad2deg*z(j,i),j=2,3)
1212         enddo
1213       endif
1214       if (lcheck) then
1215 ! Writing the distribution just to check the procedure
1216       fac=0.0D0
1217       dV=deg2rad**2*10.0D0
1218       sum=0.0D0
1219       sum1=0.0D0
1220       do i=1,nlobit
1221         fac=fac+W1(i)/detAp(i)
1222       enddo
1223       fac=1.0D0/(2.0D0*fac*pi)
1224 !d    print *,it,'fac=',fac
1225       do ial=90,180,2
1226         y(1)=deg2rad*ial
1227         do iom=-180,180,5
1228           y(2)=deg2rad*iom
1229           wart=0.0D0
1230           do i=1,nlobit
1231             do j=2,3
1232               do k=2,3
1233                 a(j-1,k-1)=gaussc(j,k,i,it)
1234               enddo
1235             enddo
1236             y2=y(2)
1237
1238             do iii=-1,1
1239
1240               y(2)=y2+iii*dwapi
1241
1242               wykl=0.0D0
1243               do j=1,2
1244                 do k=1,2
1245                   wykl=wykl+a(j,k)*(y(j)-z(j+1,i))*(y(k)-z(k+1,i))
1246                 enddo
1247               enddo
1248               wart=wart+W1(i)*dexp(-0.5D0*wykl)
1249
1250             enddo
1251
1252             y(2)=y2
1253
1254           enddo
1255 !         print *,'y',y(1),y(2),' fac=',fac
1256           wart=fac*wart
1257           write (20,'(2f10.3,1pd15.5)') y(1)*rad2deg,y(2)*rad2deg,wart
1258           sum=sum+wart
1259           sum1=sum1+1.0D0
1260         enddo
1261       enddo
1262 !     print *,'it=',it,' sum=',sum*dV,' sum1=',sum1*dV
1263       return
1264       endif
1265
1266 ! Calculate the CM of the system
1267 !
1268       do i=1,nlobit
1269         W1(i)=W1(i)/detAp(i)
1270       enddo
1271       sumW(0)=0.0D0
1272       do i=1,nlobit
1273         sumW(i)=sumW(i-1)+W1(i)
1274       enddo
1275       cm(1)=z(2,1)*W1(1)
1276       cm(2)=z(3,1)*W1(1)
1277       do j=2,nlobit
1278         cm(1)=cm(1)+z(2,j)*W1(j)
1279         cm(2)=cm(2)+W1(j)*(z(3,1)+pinorm(z(3,j)-z(3,1)))
1280       enddo
1281       cm(1)=cm(1)/sumW(nlobit)
1282       cm(2)=cm(2)/sumW(nlobit)
1283       if (cm(1).gt.Big .or. cm(1).lt.-Big .or. &
1284        cm(2).gt.Big .or. cm(2).lt.-Big) then
1285 !d        write (iout,'(a)')
1286 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1287 !d        write (iout,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1288 !d        write (*,'(a)')
1289 !d     & 'Unexpected error in GenSide - CM coordinates too large.'
1290 !d        write (*,'(i5,2(1pe14.5))') it,cm(1),cm(2)
1291         fail=.true.
1292         return
1293       endif
1294 !d    print *,'CM:',cm(1),cm(2)
1295 !
1296 ! Find the largest search distance from CM
1297 !
1298       radmax=0.0D0
1299       do i=1,nlobit
1300         do j=2,3
1301           do k=2,3
1302             a(j-1,k-1)=gaussc(j,k,i,it)
1303           enddo
1304         enddo
1305 #ifdef NAG
1306         call f02faf('N','U',2,a,3,eig,work,100,ifail)
1307 #else
1308         call djacob(2,3,10000,1.0d-10,a,vec,eig)
1309 #endif
1310 #ifdef MPI
1311         if (lprint) then
1312           print *,'*************** CG Processor',me
1313           print *,'CM:',cm(1),cm(2)
1314           write (iout,*) '*************** CG Processor',me
1315           write (iout,*) 'CM:',cm(1),cm(2)
1316           print '(A,8f10.5)','Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1317           write (iout,'(A,8f10.5)') &
1318               'Eigenvalues: ',(1.0/dsqrt(eig(k)),k=1,2)
1319         endif
1320 #endif
1321         if (eig(1).lt.eig_limit) then
1322           write(iout,'(a)') &
1323            'From Mult_Norm: Eigenvalues of A are too small.'
1324           write(*,'(a)') &
1325            'From Mult_Norm: Eigenvalues of A are too small.'
1326           fail=.true.
1327           return
1328         endif
1329         radius=0.0D0
1330 !d      print *,'i=',i
1331         do j=1,2
1332           radius=radius+pinorm(z(j+1,i)-cm(j))**2
1333         enddo
1334         radius=dsqrt(radius)+3.0D0/dsqrt(eig(1))
1335         if (radius.gt.radmax) radmax=radius
1336       enddo
1337       if (radmax.gt.pi) radmax=pi
1338 !
1339 ! Determine the boundaries of the search rectangle.
1340 !
1341       if (lprint) then
1342         print '(a,4(1pe14.4))','W1: ',(W1(i),i=1,nlob(it) )
1343         print '(a,4(1pe14.4))','radmax: ',radmax
1344       endif
1345       box(1,1)=dmax1(cm(1)-radmax,0.0D0)
1346       box(2,1)=dmin1(cm(1)+radmax,pi)
1347       box(1,2)=cm(2)-radmax
1348       box(2,2)=cm(2)+radmax
1349       if (lprint) then
1350 #ifdef MPI
1351         print *,'CG Processor',me,' Array BOX:'
1352 #else
1353         print *,'Array BOX:'
1354 #endif
1355         print '(4(1pe14.4))',((box(k,j),k=1,2),j=1,2)
1356         print '(a,4(1pe14.4))','sumW: ',(sumW(i),i=0,nlob(it) )
1357 #ifdef MPI
1358         write (iout,*)'CG Processor',me,' Array BOX:'
1359 #else
1360         write (iout,*)'Array BOX:'
1361 #endif
1362         write(iout,'(4(1pe14.4))') ((box(k,j),k=1,2),j=1,2)
1363         write(iout,'(a,4(1pe14.4))')'sumW: ',(sumW(i),i=0,nlob(it) )
1364       endif
1365 !      if (box(1,2).lt.-MaxBoxLen .or. box(2,2).gt.MaxBoxLen) then
1366 !#ifdef MPI
1367 !        write (iout,'(a,i4,a,3e15.5)') 'CG Processor:',me,': bad sampling box.',box(1,2),box(2,2),radmax
1368 !        write (*,'(a,i4,a)') 'CG Processor:',me,': bad sampling box.'
1369 !#else
1370 !        write (iout,'(a)') 'Bad sampling box.'
1371 !#endif
1372 !        fail=.true.
1373 !        return
1374 !      endif
1375       which_lobe=ran_number(0.0D0,sumW(nlobit))
1376 !     print '(a,1pe14.4)','which_lobe=',which_lobe
1377       do i=1,nlobit
1378         if (sumW(i-1).le.which_lobe .and. sumW(i).ge.which_lobe) goto 1
1379       enddo
1380     1 ilob=i
1381 !     print *,'ilob=',ilob,' nlob=',nlob(it)
1382       do i=2,3
1383         cm(i-1)=z(i,ilob)
1384         do j=2,3
1385           a(i-1,j-1)=gaussc(i,j,ilob,it)
1386         enddo
1387       enddo
1388 !d    print '(a,i4,a)','CG Processor',me,' Calling MultNorm1.'
1389       call mult_norm1(3,2,a,cm,box,y,fail)
1390       if (fail) return
1391       al=y(1)
1392       om=pinorm(y(2))
1393       else if (mnum.eq.2) then
1394        al=0.7+ran_number(0.0d0,0.2d0)
1395        om=ran_number(0.0d0,3.14d0)
1396       endif
1397
1398 !d    print *,'al=',al,' om=',om
1399 !d    stop
1400       return
1401       end subroutine gen_side
1402 !-----------------------------------------------------------------------------
1403       subroutine overlap_sc(scfail)
1404 !
1405 !     Internal and cartesian coordinates must be consistent as input,
1406 !     and will be up-to-date on return.
1407 !     At the end of this procedure, scfail is true if there are
1408 !     overlapping residues left, or false otherwise (success)
1409 !
1410 !      implicit real*8 (a-h,o-z)
1411 !      include 'DIMENSIONS'
1412 !      include 'COMMON.CHAIN'
1413 !      include 'COMMON.INTERACT'
1414 !      include 'COMMON.FFIELD'
1415 !      include 'COMMON.VAR'
1416 !      include 'COMMON.SBRIDGE'
1417 !      include 'COMMON.IOUNITS'
1418       logical :: had_overlaps,fail,scfail
1419       integer,dimension(nres) :: ioverlap !(maxres)
1420       integer :: ioverlap_last,k,maxsi,i,iti,nsi
1421       integer :: ires,j
1422
1423       had_overlaps=.false.
1424       call overlap_sc_list(ioverlap,ioverlap_last)
1425       if (ioverlap_last.gt.0) then
1426         write (iout,*) '#OVERLAPing residues ',ioverlap_last
1427         write (iout,'(20i4)') (ioverlap(k),k=1,ioverlap_last)
1428         had_overlaps=.true.
1429       endif
1430
1431       maxsi=1000
1432       do k=1,1000
1433         if (ioverlap_last.eq.0) exit
1434
1435         do ires=1,ioverlap_last
1436           i=ioverlap(ires)
1437           iti=iabs(itype(i,1))
1438           if ((iti.ne.10).and.(molnum(i).ne.5).and.(iti.ne.ntyp1)) then
1439             nsi=0
1440             fail=.true.
1441             do while (fail.and.nsi.le.maxsi)
1442               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail,molnum(i))
1443               nsi=nsi+1
1444             enddo
1445             if(fail) goto 999
1446           endif
1447         enddo
1448
1449         call chainbuild
1450         call overlap_sc_list(ioverlap,ioverlap_last)
1451 !        write (iout,*) 'Overlaping residues ',ioverlap_last,
1452 !     &           (ioverlap(j),j=1,ioverlap_last)
1453       enddo
1454
1455       if (k.le.1000.and.ioverlap_last.eq.0) then
1456         scfail=.false.
1457         if (had_overlaps) then
1458           write (iout,*) '#OVERLAPing all corrected after ',k,&
1459                ' random generation'
1460         endif
1461       else
1462         scfail=.true.
1463         write (iout,*) '#OVERLAPing NOT all corrected ',ioverlap_last
1464         write (iout,'(20i4)') (ioverlap(j),j=1,ioverlap_last)
1465       endif
1466
1467       return
1468
1469  999  continue
1470       write (iout,'(a30,i5,a12,i4)') &
1471                      '#OVERLAP FAIL in gen_side after',maxsi,&
1472                      'iter for RES',i
1473       scfail=.true.
1474       return
1475       end subroutine overlap_sc
1476 !-----------------------------------------------------------------------------
1477       subroutine overlap_sc_list(ioverlap,ioverlap_last)
1478       use calc_data
1479 !      implicit real*8 (a-h,o-z)
1480 !      include 'DIMENSIONS'
1481 !      include 'COMMON.GEO'
1482 !      include 'COMMON.LOCAL'
1483 !      include 'COMMON.IOUNITS'
1484 !      include 'COMMON.CHAIN'
1485 !      include 'COMMON.INTERACT'
1486 !      include 'COMMON.FFIELD'
1487 !      include 'COMMON.VAR'
1488 !      include 'COMMON.CALC'
1489       logical :: fail
1490       integer,dimension(nres) :: ioverlap !(maxres)
1491       integer :: ioverlap_last
1492 !el local variables
1493       integer :: ind,iint
1494       real(kind=8) :: redfac,sig        !rrij,sigsq,
1495       integer :: itypi,itypj,itypi1
1496       real(kind=8) :: xi,yi,zi,sig0ij,rcomp,rrij,rij_shift
1497       data redfac /0.5D0/
1498
1499       ioverlap_last=0
1500 ! Check for SC-SC overlaps and mark residues
1501 !      print *,'>>overlap_sc nnt=',nnt,' nct=',nct
1502       ind=0
1503       do i=iatsc_s,iatsc_e
1504         if (itype(i,molnum(i)).eq.ntyp1_molec(molnum(i))) cycle
1505         if (molnum(i).eq.5) print *,"WTF",i,iatsc_s,iatsc_e
1506         if (molnum(i).eq.5) cycle
1507         itypi=iabs(itype(i,molnum(i)))
1508         itypi1=iabs(itype(i+1,1))
1509         xi=c(1,nres+i)
1510         yi=c(2,nres+i)
1511         zi=c(3,nres+i)
1512         dxi=dc_norm(1,nres+i)
1513         dyi=dc_norm(2,nres+i)
1514         dzi=dc_norm(3,nres+i)
1515         dsci_inv=dsc_inv(itypi)
1516 !
1517        do iint=1,nint_gr(i)
1518          do j=istart(i,iint),iend(i,iint)
1519          if (itype(j,molnum(j)).eq.ntyp1_molec(molnum(j))) cycle
1520             ind=ind+1
1521             itypj=iabs(itype(j,molnum(j)))
1522             dscj_inv=dsc_inv(itypj)
1523             sig0ij=sigma(itypi,itypj)
1524             chi1=chi(itypi,itypj)
1525             chi2=chi(itypj,itypi)
1526             chi12=chi1*chi2
1527             chip1=chip(itypi)
1528             chip2=chip(itypj)
1529             chip12=chip1*chip2
1530             alf1=alp(itypi)
1531             alf2=alp(itypj)
1532             alf12=0.5D0*(alf1+alf2)
1533           if (j.gt.i+1) then
1534            rcomp=sigmaii(itypi,itypj)
1535           else
1536            rcomp=sigma(itypi,itypj)
1537           endif
1538 !         print '(2(a3,2i3),a3,2f10.5)',
1539 !     &        ' i=',i,iti,' j=',j,itj,' d=',dist(nres+i,nres+j)
1540 !     &        ,rcomp
1541             xj=c(1,nres+j)-xi
1542             yj=c(2,nres+j)-yi
1543             zj=c(3,nres+j)-zi
1544             dxj=dc_norm(1,nres+j)
1545             dyj=dc_norm(2,nres+j)
1546             dzj=dc_norm(3,nres+j)
1547             rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1548             rij=dsqrt(rrij)
1549             call sc_angular
1550             sigsq=1.0D0/sigsq
1551             sig=sig0ij*dsqrt(sigsq)
1552             rij_shift=1.0D0/rij-sig+sig0ij
1553
1554 !t          if ( 1.0/rij .lt. redfac*rcomp .or.
1555 !t     &       rij_shift.le.0.0D0 ) then
1556             if ( rij_shift.le.0.0D0 ) then
1557 !d           write (iout,'(a,i3,a,i3,a,f10.5,a,3f10.5)')
1558 !d     &     'overlap SC-SC: i=',i,' j=',j,
1559 !d     &     ' dist=',dist(nres+i,nres+j),' rcomp=',
1560 !d     &     rcomp,1.0/rij,rij_shift
1561           ioverlap_last=ioverlap_last+1
1562           ioverlap(ioverlap_last)=i
1563           do k=1,ioverlap_last-1
1564            if (ioverlap(k).eq.i) ioverlap_last=ioverlap_last-1
1565           enddo
1566           ioverlap_last=ioverlap_last+1
1567           ioverlap(ioverlap_last)=j
1568           do k=1,ioverlap_last-1
1569            if (ioverlap(k).eq.j) ioverlap_last=ioverlap_last-1
1570           enddo
1571          endif
1572         enddo
1573        enddo
1574       enddo
1575       return
1576       end subroutine overlap_sc_list
1577 #endif
1578 !-----------------------------------------------------------------------------
1579 ! energy_p_new_barrier.F
1580 !-----------------------------------------------------------------------------
1581       subroutine sc_angular
1582 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1583 ! om12. Called by ebp, egb, and egbv.
1584       use calc_data
1585 !      implicit none
1586 !      include 'COMMON.CALC'
1587 !      include 'COMMON.IOUNITS'
1588       erij(1)=xj*rij
1589       erij(2)=yj*rij
1590       erij(3)=zj*rij
1591       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1592       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1593       om12=dxi*dxj+dyi*dyj+dzi*dzj
1594       chiom12=chi12*om12
1595 ! Calculate eps1(om12) and its derivative in om12
1596       faceps1=1.0D0-om12*chiom12
1597       faceps1_inv=1.0D0/faceps1
1598       eps1=dsqrt(faceps1_inv)
1599 ! Following variable is eps1*deps1/dom12
1600       eps1_om12=faceps1_inv*chiom12
1601 ! diagnostics only
1602 !      faceps1_inv=om12
1603 !      eps1=om12
1604 !      eps1_om12=1.0d0
1605 !      write (iout,*) "om12",om12," eps1",eps1
1606 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1607 ! and om12.
1608       om1om2=om1*om2
1609       chiom1=chi1*om1
1610       chiom2=chi2*om2
1611       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1612       sigsq=1.0D0-facsig*faceps1_inv
1613       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1614       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1615       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1616 ! diagnostics only
1617 !      sigsq=1.0d0
1618 !      sigsq_om1=0.0d0
1619 !      sigsq_om2=0.0d0
1620 !      sigsq_om12=0.0d0
1621 !      write (iout,*) "chiom1",chiom1," chiom2",chiom2," chiom12",chiom12
1622 !      write (iout,*) "faceps1",faceps1," faceps1_inv",faceps1_inv,
1623 !     &    " eps1",eps1
1624 ! Calculate eps2 and its derivatives in om1, om2, and om12.
1625       chipom1=chip1*om1
1626       chipom2=chip2*om2
1627       chipom12=chip12*om12
1628       facp=1.0D0-om12*chipom12
1629       facp_inv=1.0D0/facp
1630       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1631 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1632 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1633 ! Following variable is the square root of eps2
1634       eps2rt=1.0D0-facp1*facp_inv
1635 ! Following three variables are the derivatives of the square root of eps
1636 ! in om1, om2, and om12.
1637       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1638       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1639       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1640 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1641       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1642 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1643 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1644 !     &  " eps2rt_om12",eps2rt_om12
1645 ! Calculate whole angle-dependent part of epsilon and contributions
1646 ! to its derivatives
1647       return
1648       end subroutine sc_angular
1649 !-----------------------------------------------------------------------------
1650 ! initialize_p.F
1651       subroutine sc_angular_nucl
1652 ! Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1653 ! om12. Called by ebp, egb, and egbv.
1654 !      use calc_data
1655 !      implicit none
1656 !      include 'COMMON.CALC'
1657 !      include 'COMMON.IOUNITS'
1658       use comm_locel
1659       use calc_data_nucl
1660       erij(1)=xj*rij
1661       erij(2)=yj*rij
1662       erij(3)=zj*rij
1663       om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1664       om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1665       om12=dxi*dxj+dyi*dyj+dzi*dzj
1666       chiom12=chi12*om12
1667 ! Calculate eps1(om12) and its derivative in om12
1668       faceps1=1.0D0-om12*chiom12
1669       faceps1_inv=1.0D0/faceps1
1670       eps1=dsqrt(faceps1_inv)
1671 ! Following variable is eps1*deps1/dom12
1672       eps1_om12=faceps1_inv*chiom12
1673 ! diagnostics only
1674 !      faceps1_inv=om12
1675 !      eps1=om12
1676 !      eps1_om12=1.0d0
1677 !      write (iout,*) "om12",om12," eps1",eps1
1678 ! Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1679 ! and om12.
1680       om1om2=om1*om2
1681       chiom1=chi1*om1
1682       chiom2=chi2*om2
1683       facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1684       sigsq=1.0D0-facsig*faceps1_inv
1685       sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1686       sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1687       sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1688       chipom1=chip1*om1
1689       chipom2=chip2*om2
1690       chipom12=chip12*om12
1691       facp=1.0D0-om12*chipom12
1692       facp_inv=1.0D0/facp
1693       facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1694 !      write (iout,*) "chipom1",chipom1," chipom2",chipom2,
1695 !     &  " chipom12",chipom12," facp",facp," facp_inv",facp_inv
1696 ! Following variable is the square root of eps2
1697       eps2rt=1.0D0-facp1*facp_inv
1698 ! Following three variables are the derivatives of the square root of eps
1699 ! in om1, om2, and om12.
1700       eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1701       eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1702       eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1703 ! Evaluate the "asymmetric" factor in the VDW constant, eps3
1704       eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1705 !      write (iout,*) "eps2rt",eps2rt," eps3rt",eps3rt
1706 !      write (iout,*) "eps2rt_om1",eps2rt_om1," eps2rt_om2",eps2rt_om2,
1707 !     &  " eps2rt_om12",eps2rt_om12
1708 ! Calculate whole angle-dependent part of epsilon and contributions
1709 ! to its derivatives
1710       return
1711       end subroutine sc_angular_nucl
1712
1713 !-----------------------------------------------------------------------------
1714       subroutine int_bounds(total_ints,lower_bound,upper_bound)
1715 !      implicit real*8 (a-h,o-z)
1716 !      include 'DIMENSIONS'
1717       include 'mpif.h'
1718 !      include 'COMMON.SETUP'
1719       integer :: total_ints,lower_bound,upper_bound,nint
1720       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1721       integer :: i,nexcess
1722       nint=total_ints/nfgtasks
1723       do i=1,nfgtasks
1724         int4proc(i-1)=nint
1725       enddo
1726       nexcess=total_ints-nint*nfgtasks
1727       do i=1,nexcess
1728         int4proc(nfgtasks-i)=int4proc(nfgtasks-i)+1
1729       enddo
1730       lower_bound=0
1731       do i=0,fg_rank-1
1732         lower_bound=lower_bound+int4proc(i)
1733       enddo
1734       upper_bound=lower_bound+int4proc(fg_rank)
1735       lower_bound=lower_bound+1
1736       return
1737       end subroutine int_bounds
1738 !-----------------------------------------------------------------------------
1739       subroutine int_bounds1(total_ints,lower_bound,upper_bound)
1740 !      implicit real*8 (a-h,o-z)
1741 !      include 'DIMENSIONS'
1742       include 'mpif.h'
1743 !      include 'COMMON.SETUP'
1744       integer :: total_ints,lower_bound,upper_bound,nint
1745       integer :: nexcess,i
1746       integer,dimension(0:nfgtasks) :: int4proc,sint4proc       !(0:max_fg_procs)
1747       nint=total_ints/nfgtasks1
1748       do i=1,nfgtasks1
1749         int4proc(i-1)=nint
1750       enddo
1751       nexcess=total_ints-nint*nfgtasks1
1752       do i=1,nexcess
1753         int4proc(nfgtasks1-i)=int4proc(nfgtasks1-i)+1
1754       enddo
1755       lower_bound=0
1756       do i=0,fg_rank1-1
1757         lower_bound=lower_bound+int4proc(i)
1758       enddo
1759       upper_bound=lower_bound+int4proc(fg_rank1)
1760       lower_bound=lower_bound+1
1761       return
1762       end subroutine int_bounds1
1763 !-----------------------------------------------------------------------------
1764 ! intcartderiv.F
1765 !-----------------------------------------------------------------------------
1766       subroutine chainbuild_cart
1767 !      implicit real*8 (a-h,o-z)
1768 !      include 'DIMENSIONS'
1769       use control_data
1770 #ifdef MPI
1771       include 'mpif.h'
1772 #endif
1773 !      include 'COMMON.SETUP'
1774 !      include 'COMMON.CHAIN'
1775 !      include 'COMMON.LOCAL'
1776 !      include 'COMMON.TIME1'
1777 !      include 'COMMON.IOUNITS'
1778       integer :: j,i,ierror,ierr
1779       real(kind=8) :: time00,time01
1780 #ifdef MPI
1781       if (nfgtasks.gt.1) then
1782 !        write (iout,*) "BCAST in chainbuild_cart"
1783 !        call flush(iout)
1784 ! Broadcast the order to build the chain and compute internal coordinates
1785 ! to the slaves. The slaves receive the order in ERGASTULUM.
1786         time00=MPI_Wtime()
1787 !      write (iout,*) "CHAINBUILD_CART: DC before 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         if (fg_rank.eq.0) &
1793           call MPI_Bcast(7,1,MPI_INTEGER,king,FG_COMM,IERROR)
1794         time_bcast7=time_bcast7+MPI_Wtime()-time00
1795         time01=MPI_Wtime()
1796         call MPI_Bcast(dc(1,0),6*(nres+1),MPI_DOUBLE_PRECISION,&
1797           king,FG_COMM,IERR)
1798 !      write (iout,*) "CHAINBUILD_CART: DC after BCAST"
1799 !      do i=0,nres
1800 !        write (iout,'(i3,3f10.5,5x,3f10.5)') i,(dc(j,i),j=1,3),
1801 !     &   (dc(j,i+nres),j=1,3)
1802 !      enddo
1803 !        write (iout,*) "End BCAST in chainbuild_cart"
1804 !        call flush(iout)
1805         time_bcast=time_bcast+MPI_Wtime()-time00
1806         time_bcastc=time_bcastc+MPI_Wtime()-time01
1807       endif
1808 #endif
1809       do j=1,3
1810         c(j,1)=dc(j,0)
1811       enddo
1812       do i=2,nres
1813         do j=1,3
1814           c(j,i)=c(j,i-1)+dc(j,i-1)
1815         enddo
1816       enddo
1817       do i=1,nres
1818         do j=1,3
1819           c(j,i+nres)=c(j,i)+dc(j,i+nres)
1820         enddo
1821       enddo
1822 !      write (iout,*) "CHAINBUILD_CART"
1823 !      call cartprint
1824       call int_from_cart1(.false.)
1825       return
1826       end subroutine chainbuild_cart
1827 !-----------------------------------------------------------------------------
1828 ! intcor.f
1829 !-----------------------------------------------------------------------------
1830       real(kind=8) function alpha(i1,i2,i3)
1831 !
1832 !  Calculates the planar angle between atoms (i1), (i2), and (i3).
1833 !
1834 !      implicit real*8 (a-h,o-z)
1835 !      include 'DIMENSIONS'
1836 !      include 'COMMON.GEO'
1837 !      include 'COMMON.CHAIN'
1838 !el local variables
1839       integer :: i1,i2,i3
1840       real(kind=8) :: x12,x23,y12,y23,z12,z23,vnorm,wnorm,scalar
1841       x12=c(1,i1)-c(1,i2)
1842       x23=c(1,i3)-c(1,i2)
1843       y12=c(2,i1)-c(2,i2)
1844       y23=c(2,i3)-c(2,i2)
1845       z12=c(3,i1)-c(3,i2)
1846       z23=c(3,i3)-c(3,i2)
1847       vnorm=dsqrt(x12*x12+y12*y12+z12*z12)
1848       wnorm=dsqrt(x23*x23+y23*y23+z23*z23)
1849       scalar=(x12*x23+y12*y23+z12*z23)/(vnorm*wnorm)
1850       alpha=arcos(scalar)
1851       return
1852       end function alpha
1853 !-----------------------------------------------------------------------------
1854       real(kind=8) function beta(i1,i2,i3,i4)
1855 !
1856 !  Calculates the dihedral angle between atoms (i1), (i2), (i3) and (i4)
1857 !
1858 !      implicit real*8 (a-h,o-z)
1859 !      include 'DIMENSIONS'
1860 !      include 'COMMON.GEO'
1861 !      include 'COMMON.CHAIN'
1862 !el local variables
1863       integer :: i1,i2,i3,i4
1864       real(kind=8) :: x12,x23,x34,y12,y23,y34,z12,z23,z34
1865       real(kind=8) :: wx,wy,wz,wnorm,vx,vy,vz,vnorm,scalar,angle
1866       real(kind=8) :: tx,ty,tz
1867       x12=c(1,i1)-c(1,i2)
1868       x23=c(1,i3)-c(1,i2)
1869       x34=c(1,i4)-c(1,i3)
1870       y12=c(2,i1)-c(2,i2)
1871       y23=c(2,i3)-c(2,i2)
1872       y34=c(2,i4)-c(2,i3)
1873       z12=c(3,i1)-c(3,i2)
1874       z23=c(3,i3)-c(3,i2)
1875       z34=c(3,i4)-c(3,i3)
1876 !d    print '(2i3,3f10.5)',i1,i2,x12,y12,z12
1877 !d    print '(2i3,3f10.5)',i2,i3,x23,y23,z23
1878 !d    print '(2i3,3f10.5)',i3,i4,x34,y34,z34
1879       wx=-y23*z34+y34*z23
1880       wy=x23*z34-z23*x34
1881       wz=-x23*y34+y23*x34
1882       wnorm=dsqrt(wx*wx+wy*wy+wz*wz)
1883       vx=y12*z23-z12*y23
1884       vy=-x12*z23+z12*x23
1885       vz=x12*y23-y12*x23
1886       vnorm=dsqrt(vx*vx+vy*vy+vz*vz)
1887       if (vnorm.gt.1.0D-13 .and. wnorm.gt.1.0D-13) then
1888       scalar=(vx*wx+vy*wy+vz*wz)/(vnorm*wnorm)
1889       if (dabs(scalar).gt.1.0D0) &
1890       scalar=0.99999999999999D0*scalar/dabs(scalar)
1891       angle=dacos(scalar)
1892 !d    print '(2i4,10f7.3)',i2,i3,vx,vy,vz,wx,wy,wz,vnorm,wnorm,
1893 !d   &scalar,angle
1894       else
1895       angle=pi
1896       endif
1897 !     if (angle.le.0.0D0) angle=pi+angle
1898       tx=vy*wz-vz*wy
1899       ty=-vx*wz+vz*wx
1900       tz=vx*wy-vy*wx
1901       scalar=tx*x23+ty*y23+tz*z23
1902       if (scalar.lt.0.0D0) angle=-angle
1903       beta=angle
1904       return
1905       end function beta
1906 !-----------------------------------------------------------------------------
1907       real(kind=8) function dist(i1,i2)
1908 !
1909 !  Calculates the distance between atoms (i1) and (i2).
1910 !
1911 !      implicit real*8 (a-h,o-z)
1912 !      include 'DIMENSIONS'
1913 !      include 'COMMON.GEO'
1914 !      include 'COMMON.CHAIN'
1915 !el local variables
1916       integer :: i1,i2
1917       real(kind=8) :: x12,y12,z12
1918       x12=c(1,i1)-c(1,i2)
1919       y12=c(2,i1)-c(2,i2)
1920       z12=c(3,i1)-c(3,i2)
1921       dist=dsqrt(x12*x12+y12*y12+z12*z12)
1922       return
1923       end function dist
1924 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
1925 !-----------------------------------------------------------------------------
1926 ! local_move.f
1927 !-----------------------------------------------------------------------------
1928       subroutine local_move_init(debug)
1929 !rc      implicit none
1930
1931 !     Includes
1932 !      implicit real*8 (a-h,o-z)
1933 !      include 'DIMENSIONS'  ! Needed by COMMON.LOCAL
1934 !      include 'COMMON.GEO'  ! For pi, deg2rad
1935 !      include 'COMMON.LOCAL'  ! For vbl
1936 !      include 'COMMON.LOCMOVE'
1937
1938 !     INPUT arguments
1939       logical :: debug
1940
1941
1942 !     Determine wheter to do some debugging output
1943       locmove_output=debug
1944
1945 !     Set the init_called flag to 1
1946       init_called=1
1947
1948 !     The following are never changed
1949       min_theta=60.D0*deg2rad  ! (0,PI)
1950       max_theta=175.D0*deg2rad  ! (0,PI)
1951       dmin2=vbl*vbl*2.*(1.-cos(min_theta))
1952       dmax2=vbl*vbl*2.*(1.-cos(max_theta))
1953       flag=1.0D300
1954       small=1.0D-5
1955       small2=0.5*small*small
1956
1957 !     Not really necessary...
1958       a_n=0
1959       b_n=0
1960       res_n=0
1961
1962       return
1963       end subroutine local_move_init
1964 !-----------------------------------------------------------------------------
1965       subroutine local_move(n_start, n_end, PHImin, PHImax)
1966 !     Perform a local move between residues m and n (inclusive)
1967 !     PHImin and PHImax [0,PI] determine the size of the move
1968 !     Works on whatever structure is in the variables theta and phi,
1969 !     sidechain variables are left untouched
1970 !     The final structure is NOT minimized, but both the cartesian
1971 !     variables c and the angles are up-to-date at the end (no further
1972 !     chainbuild is required)
1973 !rc      implicit none
1974       use random,only:ran_number
1975 !     Includes
1976 !      implicit real*8 (a-h,o-z)
1977 !      include 'DIMENSIONS'
1978 !      include 'COMMON.GEO'
1979 !      include 'COMMON.CHAIN'
1980 !      include 'COMMON.VAR'
1981 !      include 'COMMON.MINIM'
1982 !      include 'COMMON.SBRIDGE'
1983 !      include 'COMMON.LOCMOVE'
1984
1985 !     External functions
1986 !EL      integer move_res
1987 !EL      external move_res
1988 !EL      double precision ran_number
1989 !EL      external ran_number
1990
1991 !     INPUT arguments
1992       integer :: n_start, n_end  ! First and last residues to move
1993       real(kind=8) :: PHImin, PHImax  ! min/max angles [0,PI]
1994
1995 !     Local variables
1996       integer :: i,j
1997       real(kind=8) :: min,max
1998       integer :: iretcode
1999
2000
2001 !     Check if local_move_init was called.  This assumes that it
2002 !     would not be 1 if not explicitely initialized
2003       if (init_called.ne.1) then
2004         write(6,*)'   ***   local_move_init not called!!!'
2005         stop
2006       endif
2007
2008 !     Quick check for crazy range
2009       if (n_start.gt.n_end .or. n_start.lt.1 .or. n_end.gt.nres) then
2010         write(6,'(a,i3,a,i3)') &
2011              '   ***   Cannot make local move between n_start = ',&
2012              n_start,' and n_end = ',n_end
2013         return
2014       endif
2015
2016 !     Take care of end residues first...
2017       if (n_start.eq.1) then
2018 !     Move residue 1 (completely random)
2019         theta(3)=ran_number(min_theta,max_theta)
2020         phi(4)=ran_number(-PI,PI)
2021         i=2
2022       else
2023         i=n_start
2024       endif
2025       if (n_end.eq.nres) then
2026 !     Move residue nres (completely random)
2027         theta(nres)=ran_number(min_theta,max_theta)
2028         phi(nres)=ran_number(-PI,PI)
2029         j=nres-1
2030       else
2031         j=n_end
2032       endif
2033
2034 !     ...then go through all other residues one by one
2035 !     Start from the two extremes and converge
2036       call chainbuild
2037       do while (i.le.j)
2038         min=PHImin
2039         max=PHImax
2040 !$$$c     Move the first two residues by less than the others
2041 !$$$        if (i-n_start.lt.3) then
2042 !$$$          if (i-n_start.eq.0) then
2043 !$$$            min=0.4*PHImin
2044 !$$$            max=0.4*PHImax
2045 !$$$          else if (i-n_start.eq.1) then
2046 !$$$            min=0.8*PHImin
2047 !$$$            max=0.8*PHImax
2048 !$$$          else if (i-n_start.eq.2) then
2049 !$$$            min=PHImin
2050 !$$$            max=PHImax
2051 !$$$          endif
2052 !$$$        endif
2053
2054 !     The actual move, on residue i
2055         iretcode=move_res(min,max,i)  ! Discard iretcode
2056         i=i+1
2057
2058         if (i.le.j) then
2059           min=PHImin
2060           max=PHImax
2061 !$$$c     Move the last two residues by less than the others
2062 !$$$          if (n_end-j.lt.3) then
2063 !$$$            if (n_end-j.eq.0) then
2064 !$$$              min=0.4*PHImin
2065 !$$$              max=0.4*PHImax
2066 !$$$            else if (n_end-j.eq.1) then
2067 !$$$              min=0.8*PHImin
2068 !$$$              max=0.8*PHImax
2069 !$$$            else if (n_end-j.eq.2) then
2070 !$$$              min=PHImin
2071 !$$$              max=PHImax
2072 !$$$            endif
2073 !$$$          endif
2074
2075 !     The actual move, on residue j
2076           iretcode=move_res(min,max,j)  ! Discard iretcode
2077           j=j-1
2078         endif
2079       enddo
2080
2081       call int_from_cart(.false.,.false.)
2082
2083       return
2084       end subroutine local_move
2085 !-----------------------------------------------------------------------------
2086       subroutine output_tabs
2087 !     Prints out the contents of a_..., b_..., res_...
2088 !      implicit none
2089
2090 !     Includes
2091 !      include 'COMMON.GEO'
2092 !      include 'COMMON.LOCMOVE'
2093
2094 !     Local variables
2095       integer :: i,j
2096
2097       write(6,*)'a_...'
2098       write(6,'(8f7.1)')(a_ang(i)*rad2deg,i=0,a_n-1)
2099       write(6,'(8(2x,3l1,2x))')((a_tab(i,j),i=0,2),j=0,a_n-1)
2100
2101       write(6,*)'b_...'
2102       write(6,'(4f7.1)')(b_ang(i)*rad2deg,i=0,b_n-1)
2103       write(6,'(4(2x,3l1,2x))')((b_tab(i,j),i=0,2),j=0,b_n-1)
2104
2105       write(6,*)'res_...'
2106       write(6,'(12f7.1)')(res_ang(i)*rad2deg,i=0,res_n-1)
2107       write(6,'(12(2x,3l1,2x))')((res_tab(0,i,j),i=0,2),j=0,res_n-1)
2108       write(6,'(12(2x,3l1,2x))')((res_tab(1,i,j),i=0,2),j=0,res_n-1)
2109       write(6,'(12(2x,3l1,2x))')((res_tab(2,i,j),i=0,2),j=0,res_n-1)
2110
2111       return
2112       end subroutine output_tabs
2113 !-----------------------------------------------------------------------------
2114       subroutine angles2tab(PHImin,PHImax,n,ang,tab)
2115 !     Only uses angles if [0,PI] (but PHImin cannot be 0.,
2116 !     and PHImax cannot be PI)
2117 !      implicit none
2118
2119 !     Includes
2120 !      include 'COMMON.GEO'
2121
2122 !     INPUT arguments
2123       real(kind=8) :: PHImin,PHImax
2124
2125 !     OUTPUT arguments
2126       integer :: n
2127       real(kind=8),dimension(0:3) :: ang
2128       logical,dimension(0:2,0:3) :: tab
2129
2130
2131       if (PHImin .eq. PHImax) then
2132 !     Special case with two 010's
2133         n = 2;
2134         ang(0) = -PHImin;
2135         ang(1) = PHImin;
2136         tab(0,0) = .false.
2137         tab(2,0) = .false.
2138         tab(0,1) = .false.
2139         tab(2,1) = .false.
2140         tab(1,0) = .true.
2141         tab(1,1) = .true.
2142       else if (PHImin .eq. PI) then
2143 !     Special case with one 010
2144         n = 1
2145         ang(0) = PI
2146         tab(0,0) = .false.
2147         tab(2,0) = .false.
2148         tab(1,0) = .true.
2149       else if (PHImax .eq. 0.) then
2150 !     Special case with one 010
2151         n = 1
2152         ang(0) = 0.
2153         tab(0,0) = .false.
2154         tab(2,0) = .false.
2155         tab(1,0) = .true.
2156       else
2157 !     Standard cases
2158         n = 0
2159         if (PHImin .gt. 0.) then
2160 !     Start of range (011)
2161           ang(n) = PHImin
2162           tab(0,n) = .false.
2163           tab(1,n) = .true.
2164           tab(2,n) = .true.
2165 !     End of range (110)
2166           ang(n+1) = -PHImin
2167           tab(0,n+1) = .true.
2168           tab(1,n+1) = .true.
2169           tab(2,n+1) = .false.
2170           n = n+2
2171         endif
2172         if (PHImax .lt. PI) then
2173 !     Start of range (011)
2174           ang(n) = -PHImax
2175           tab(0,n) = .false.
2176           tab(1,n) = .true.
2177           tab(2,n) = .true.
2178 !     End of range (110)
2179           ang(n+1) = PHImax
2180           tab(0,n+1) = .true.
2181           tab(1,n+1) = .true.
2182           tab(2,n+1) = .false.
2183           n = n+2
2184         endif
2185       endif
2186
2187       return
2188       end subroutine angles2tab
2189 !-----------------------------------------------------------------------------
2190       subroutine minmax_angles(x,y,z,r,n,ang,tab)
2191 !     When solutions do not exist, assume all angles
2192 !     are acceptable - i.e., initial geometry must be correct
2193 !      implicit none
2194
2195 !     Includes
2196 !      include 'COMMON.GEO'
2197 !      include 'COMMON.LOCMOVE'
2198
2199 !     Input arguments
2200       real(kind=8) :: x,y,z,r
2201
2202 !     Output arguments
2203       integer :: n
2204       real(kind=8),dimension(0:3) :: ang
2205       logical,dimension(0:2,0:3) :: tab
2206
2207 !     Local variables
2208       real(kind=8) :: num, denom, phi
2209       real(kind=8) :: Kmin, Kmax
2210       integer :: i
2211
2212
2213       num = x*x + y*y + z*z
2214       denom = x*x + y*y
2215       n = 0
2216       if (denom .gt. 0.) then
2217         phi = atan2(y,x)
2218         denom = 2.*r*sqrt(denom)
2219         num = num+r*r
2220         Kmin = (num - dmin2)/denom
2221         Kmax = (num - dmax2)/denom
2222
2223 !     Allowed values of K (else all angles are acceptable)
2224 !     -1 <= Kmin <  1
2225 !     -1 <  Kmax <= 1
2226         if (Kmin .gt. 1. .or. abs(Kmin-1.) .lt. small2) then
2227           Kmin = -flag
2228         else if (Kmin .lt. -1. .or. abs(Kmin+1.) .lt. small2) then
2229           Kmin = PI
2230         else
2231           Kmin = acos(Kmin)
2232         endif
2233
2234         if (Kmax .lt. -1. .or. abs(Kmax+1.) .lt. small2) then
2235           Kmax = flag
2236         else if (Kmax .gt. 1. .or. abs(Kmax-1.) .lt. small2) then
2237           Kmax = 0.
2238         else
2239           Kmax = acos(Kmax)
2240         endif
2241
2242         if (Kmax .lt. Kmin) Kmax = Kmin
2243
2244         call angles2tab(Kmin, Kmax, n, ang, tab)
2245
2246 !     Add phi and check that angles are within range (-PI,PI]
2247         do i=0,n-1
2248           ang(i) = ang(i)+phi
2249           if (ang(i) .le. -PI) then
2250             ang(i) = ang(i)+2.*PI
2251           else if (ang(i) .gt. PI) then
2252             ang(i) = ang(i)-2.*PI
2253           endif
2254         enddo
2255       endif
2256
2257       return
2258       end subroutine minmax_angles
2259 !-----------------------------------------------------------------------------
2260       subroutine construct_tab
2261 !     Take a_... and b_... values and produces the results res_...
2262 !     x_ang are assumed to be all different (diff > small)
2263 !     x_tab(1,i) must be 1 for all i (i.e., all x_ang are acceptable)
2264 !      implicit none
2265
2266 !     Includes
2267 !      include 'COMMON.LOCMOVE'
2268
2269 !     Local variables
2270       integer :: n_max,i,j,index
2271       logical :: done
2272       real(kind=8) :: phi
2273
2274
2275       n_max = a_n + b_n
2276       if (n_max .eq. 0) then
2277         res_n = 0
2278         return
2279       endif
2280
2281       do i=0,n_max-1
2282         do j=0,1
2283           res_tab(j,0,i) = .true.
2284           res_tab(j,2,i) = .true.
2285           res_tab(j,1,i) = .false.
2286         enddo
2287       enddo
2288
2289       index = 0
2290       phi = -flag
2291       done = .false.
2292       do while (.not.done)
2293         res_ang(index) = flag
2294
2295 !     Check a first...
2296         do i=0,a_n-1
2297           if ((a_ang(i)-phi).gt.small .and. &
2298                a_ang(i) .lt. res_ang(index)) then
2299 !     Found a lower angle
2300             res_ang(index) = a_ang(i)
2301 !     Copy the values from a_tab into res_tab(0,,)
2302             res_tab(0,0,index) = a_tab(0,i)
2303             res_tab(0,1,index) = a_tab(1,i)
2304             res_tab(0,2,index) = a_tab(2,i)
2305 !     Set default values for res_tab(1,,)
2306             res_tab(1,0,index) = .true.
2307             res_tab(1,1,index) = .false.
2308             res_tab(1,2,index) = .true.
2309           else if (abs(a_ang(i)-res_ang(index)).lt.small) then
2310 !     Found an equal angle (can only be equal to a b_ang)
2311             res_tab(0,0,index) = a_tab(0,i)
2312             res_tab(0,1,index) = a_tab(1,i)
2313             res_tab(0,2,index) = a_tab(2,i)
2314           endif
2315         enddo
2316 !     ...then check b
2317         do i=0,b_n-1
2318           if ((b_ang(i)-phi).gt.small .and. &
2319                b_ang(i) .lt. res_ang(index)) then
2320 !     Found a lower angle
2321             res_ang(index) = b_ang(i)
2322 !     Copy the values from b_tab into res_tab(1,,)
2323             res_tab(1,0,index) = b_tab(0,i)
2324             res_tab(1,1,index) = b_tab(1,i)
2325             res_tab(1,2,index) = b_tab(2,i)
2326 !     Set default values for res_tab(0,,)
2327             res_tab(0,0,index) = .true.
2328             res_tab(0,1,index) = .false.
2329             res_tab(0,2,index) = .true.
2330           else if (abs(b_ang(i)-res_ang(index)).lt.small) then
2331 !     Found an equal angle (can only be equal to an a_ang)
2332             res_tab(1,0,index) = b_tab(0,i)
2333             res_tab(1,1,index) = b_tab(1,i)
2334             res_tab(1,2,index) = b_tab(2,i)
2335           endif
2336         enddo
2337
2338         if (res_ang(index) .eq. flag) then
2339           res_n = index
2340           done = .true.
2341         else if (index .eq. n_max-1) then
2342           res_n = n_max
2343           done = .true.
2344         else
2345           phi = res_ang(index)  ! Store previous angle
2346           index = index+1
2347         endif
2348       enddo
2349
2350 !     Fill the gaps
2351 !     First a...
2352       index = 0
2353       if (a_n .gt. 0) then
2354         do while (.not.res_tab(0,1,index))
2355           index=index+1
2356         enddo
2357         done = res_tab(0,2,index)
2358         do i=index+1,res_n-1
2359           if (res_tab(0,1,i)) then
2360             done = res_tab(0,2,i)
2361           else
2362             res_tab(0,0,i) = done
2363             res_tab(0,1,i) = done
2364             res_tab(0,2,i) = done
2365           endif
2366         enddo
2367         done = res_tab(0,0,index)
2368         do i=index-1,0,-1
2369           if (res_tab(0,1,i)) then
2370             done = res_tab(0,0,i)
2371           else
2372             res_tab(0,0,i) = done
2373             res_tab(0,1,i) = done
2374             res_tab(0,2,i) = done
2375           endif
2376         enddo
2377       else
2378         do i=0,res_n-1
2379           res_tab(0,0,i) = .true.
2380           res_tab(0,1,i) = .true.
2381           res_tab(0,2,i) = .true.
2382         enddo
2383       endif
2384 !     ...then b
2385       index = 0
2386       if (b_n .gt. 0) then
2387         do while (.not.res_tab(1,1,index))
2388           index=index+1
2389         enddo
2390         done = res_tab(1,2,index)
2391         do i=index+1,res_n-1
2392           if (res_tab(1,1,i)) then
2393             done = res_tab(1,2,i)
2394           else
2395             res_tab(1,0,i) = done
2396             res_tab(1,1,i) = done
2397             res_tab(1,2,i) = done
2398           endif
2399         enddo
2400         done = res_tab(1,0,index)
2401         do i=index-1,0,-1
2402           if (res_tab(1,1,i)) then
2403             done = res_tab(1,0,i)
2404           else
2405             res_tab(1,0,i) = done
2406             res_tab(1,1,i) = done
2407             res_tab(1,2,i) = done
2408           endif
2409         enddo
2410       else
2411         do i=0,res_n-1
2412           res_tab(1,0,i) = .true.
2413           res_tab(1,1,i) = .true.
2414           res_tab(1,2,i) = .true.
2415         enddo
2416       endif
2417
2418 !     Finally fill the last row with AND operation
2419       do i=0,res_n-1
2420         do j=0,2
2421           res_tab(2,j,i) = (res_tab(0,j,i) .and. res_tab(1,j,i))
2422         enddo
2423       enddo
2424
2425       return
2426       end subroutine construct_tab
2427 !-----------------------------------------------------------------------------
2428       subroutine construct_ranges(phi_n,phi_start,phi_end)
2429 !     Given the data in res_..., construct a table of
2430 !     min/max allowed angles
2431 !      implicit none
2432
2433 !     Includes
2434 !      include 'COMMON.GEO'
2435 !      include 'COMMON.LOCMOVE'
2436
2437 !     Output arguments
2438       integer :: phi_n
2439       real(kind=8),dimension(0:11) :: phi_start,phi_end
2440
2441 !     Local variables
2442       logical :: done
2443       integer :: index
2444
2445
2446       if (res_n .eq. 0) then
2447 !     Any move is allowed
2448         phi_n = 1
2449         phi_start(0) = -PI
2450         phi_end(0) = PI
2451       else
2452         phi_n = 0
2453         index = 0
2454         done = .false.
2455         do while (.not.done)
2456 !     Find start of range (01x)
2457           done = .false.
2458           do while (.not.done)
2459             if (res_tab(2,0,index).or.(.not.res_tab(2,1,index))) then
2460               index=index+1
2461             else
2462               done = .true.
2463               phi_start(phi_n) = res_ang(index)
2464             endif
2465             if (index .eq. res_n) done = .true.
2466           enddo
2467 !     If a start was found (index < res_n), find the end of range (x10)
2468 !     It may not be found without wrapping around
2469           if (index .lt. res_n) then
2470             done = .false.
2471             do while (.not.done)
2472               if ((.not.res_tab(2,1,index)).or.res_tab(2,2,index)) then
2473                 index=index+1
2474               else
2475                 done = .true.
2476               endif
2477               if (index .eq. res_n) done = .true.
2478             enddo
2479             if (index .lt. res_n) then
2480 !     Found the end of the range
2481               phi_end(phi_n) = res_ang(index)
2482               phi_n=phi_n+1
2483               index=index+1
2484               if (index .eq. res_n) then
2485                 done = .true.
2486               else
2487                 done = .false.
2488               endif
2489             else
2490 !     Need to wrap around
2491               done = .true.
2492               phi_end(phi_n) = flag
2493             endif
2494           endif
2495         enddo
2496 !     Take care of the last one if need to wrap around
2497         if (phi_end(phi_n) .eq. flag) then
2498           index = 0
2499           do while ((.not.res_tab(2,1,index)).or.res_tab(2,2,index))
2500             index=index+1
2501           enddo
2502           phi_end(phi_n) = res_ang(index) + 2.*PI
2503           phi_n=phi_n+1
2504         endif
2505       endif
2506
2507       return
2508       end subroutine construct_ranges
2509 !-----------------------------------------------------------------------------
2510       subroutine fix_no_moves(phi)
2511 !      implicit none
2512
2513 !     Includes
2514 !      include 'COMMON.GEO'
2515 !      include 'COMMON.LOCMOVE'
2516
2517 !     Output arguments
2518       real(kind=8) :: phi
2519
2520 !     Local variables
2521       integer :: index
2522       real(kind=8) :: diff,temp
2523
2524
2525 !     Look for first 01x in gammas (there MUST be at least one)
2526       diff = flag
2527       index = 0
2528       do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2529         index=index+1
2530       enddo
2531       if (res_ang(index) .le. 0.D0) then ! Make sure it's from PHImax
2532 !     Try to increase PHImax
2533         if (index .gt. 0) then
2534           phi = res_ang(index-1)
2535           diff = abs(res_ang(index) - res_ang(index-1))
2536         endif
2537 !     Look for last (corresponding) x10
2538         index = res_n - 1
2539         do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2540           index=index-1
2541         enddo
2542         if (index .lt. res_n-1) then
2543           temp = abs(res_ang(index) - res_ang(index+1))
2544           if (temp .lt. diff) then
2545             phi = res_ang(index+1)
2546             diff = temp
2547           endif
2548         endif
2549       endif
2550
2551 !     If increasing PHImax didn't work, decreasing PHImin
2552 !     will (with one exception)
2553 !     Look for first x10 (there MUST be at least one)
2554       index = 0
2555       do while ((.not.res_tab(1,1,index)) .or. res_tab(1,2,index))
2556         index=index+1
2557       enddo
2558       if (res_ang(index) .lt. 0.D0) then ! Make sure it's from PHImin
2559 !     Try to decrease PHImin
2560         if (index .lt. res_n-1) then
2561           temp = abs(res_ang(index) - res_ang(index+1))
2562           if (res_ang(index+1) .le. 0.D0 .and. temp .lt. diff) then
2563             phi = res_ang(index+1)
2564             diff = temp
2565           endif
2566         endif
2567 !     Look for last (corresponding) 01x
2568         index = res_n - 1
2569         do while (res_tab(1,0,index) .or. (.not.res_tab(1,1,index)))
2570           index=index-1
2571         enddo
2572         if (index .gt. 0) then
2573           temp = abs(res_ang(index) - res_ang(index-1))
2574           if (res_ang(index-1) .ge. 0.D0 .and. temp .lt. diff) then
2575             phi = res_ang(index-1)
2576             diff = temp
2577           endif
2578         endif
2579       endif
2580
2581 !     If it still didn't work, it must be PHImax == 0. or PHImin == PI
2582       if (diff .eq. flag) then
2583         index = 0
2584         if (res_tab(index,1,0) .or. (.not.res_tab(index,1,1)) .or. &
2585              res_tab(index,1,2)) index = res_n - 1
2586 !     This MUST work at this point
2587         if (index .eq. 0) then
2588           phi = res_ang(1)
2589         else
2590           phi = res_ang(index - 1)
2591         endif
2592       endif
2593
2594       return
2595       end subroutine fix_no_moves
2596 !-----------------------------------------------------------------------------
2597       integer function move_res(PHImin,PHImax,i_move)
2598 !     Moves residue i_move (in array c), leaving everything else fixed
2599 !     Starting geometry is not checked, it should be correct!
2600 !     R(,i_move) is the only residue that will move, but must have
2601 !     1 < i_move < nres (i.e., cannot move ends)
2602 !     Whether any output is done is controlled by locmove_output
2603 !rc      implicit none
2604       use random,only:ran_number
2605 !     Includes
2606 !      implicit real*8 (a-h,o-z)
2607 !      include 'DIMENSIONS'
2608 !      include 'COMMON.CHAIN'
2609 !      include 'COMMON.GEO'
2610 !      include 'COMMON.LOCMOVE'
2611
2612 !     External functions
2613 !EL      double precision ran_number
2614 !EL      external ran_number
2615
2616 !     Input arguments
2617       real(kind=8) :: PHImin,PHImax
2618       integer :: i_move
2619
2620 !     RETURN VALUES:
2621 !     0: move successfull
2622 !     1: Dmin or Dmax had to be modified
2623 !     2: move failed - check your input geometry
2624
2625
2626 !     Local variables
2627       real(kind=8),dimension(0:2) :: X,Y,Z,Orig
2628       real(kind=8),dimension(0:2) :: P
2629       logical :: no_moves,done
2630       integer :: index,i,j
2631       real(kind=8) :: phi,temp,radius
2632       real(kind=8),dimension(0:11) :: phi_start,phi_end
2633       integer :: phi_n
2634
2635 !     Set up the coordinate system
2636       do i=0,2
2637         Orig(i)=0.5*(c(i+1,i_move-1)+c(i+1,i_move+1)) ! Position of origin
2638       enddo
2639
2640       do i=0,2
2641         Z(i)=c(i+1,i_move+1)-c(i+1,i_move-1)
2642       enddo
2643       temp=sqrt(Z(0)*Z(0)+Z(1)*Z(1)+Z(2)*Z(2))
2644       do i=0,2
2645         Z(i)=Z(i)/temp
2646       enddo
2647
2648       do i=0,2
2649         X(i)=c(i+1,i_move)-Orig(i)
2650       enddo
2651 !     radius is the radius of the circle on which c(,i_move) can move
2652       radius=sqrt(X(0)*X(0)+X(1)*X(1)+X(2)*X(2))
2653       do i=0,2
2654         X(i)=X(i)/radius
2655       enddo
2656
2657       Y(0)=Z(1)*X(2)-X(1)*Z(2)
2658       Y(1)=X(0)*Z(2)-Z(0)*X(2)
2659       Y(2)=Z(0)*X(1)-X(0)*Z(1)
2660
2661 !     Calculate min, max angles coming from dmin, dmax to c(,i_move-2)
2662       if (i_move.gt.2) then
2663         do i=0,2
2664           P(i)=c(i+1,i_move-2)-Orig(i)
2665         enddo
2666         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2667              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2668              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2669              radius,a_n,a_ang,a_tab)
2670       else
2671         a_n=0
2672       endif
2673
2674 !     Calculate min, max angles coming from dmin, dmax to c(,i_move+2)
2675       if (i_move.lt.nres-2) then
2676         do i=0,2
2677           P(i)=c(i+1,i_move+2)-Orig(i)
2678         enddo
2679         call minmax_angles(P(0)*X(0)+P(1)*X(1)+P(2)*X(2),&
2680              P(0)*Y(0)+P(1)*Y(1)+P(2)*Y(2),&
2681              P(0)*Z(0)+P(1)*Z(1)+P(2)*Z(2),&
2682              radius,b_n,b_ang,b_tab)
2683       else
2684         b_n=0
2685       endif
2686
2687 !     Construct the resulting table for alpha and beta
2688       call construct_tab()
2689
2690       if (locmove_output) then
2691         print *,'ALPHAS & BETAS TABLE'
2692         call output_tabs()
2693       endif
2694
2695 !     Check that there is at least one possible move
2696       no_moves = .true.
2697       if (res_n .eq. 0) then
2698         no_moves = .false.
2699       else
2700         index = 0
2701         do while ((index .lt. res_n) .and. no_moves)
2702           if (res_tab(2,1,index)) no_moves = .false.
2703           index=index+1
2704         enddo
2705       endif
2706       if (no_moves) then
2707         if (locmove_output) print *,'   ***   Cannot move anywhere'
2708         move_res=2
2709         return
2710       endif
2711
2712 !     Transfer res_... into a_...
2713       a_n = 0
2714       do i=0,res_n-1
2715         if ( (res_tab(2,0,i).neqv.res_tab(2,1,i)) .or. &
2716              (res_tab(2,0,i).neqv.res_tab(2,2,i)) ) then
2717           a_ang(a_n) = res_ang(i)
2718           do j=0,2
2719             a_tab(j,a_n) = res_tab(2,j,i)
2720           enddo
2721           a_n=a_n+1
2722         endif
2723       enddo
2724
2725 !     Check that the PHI's are within [0,PI]
2726       if (PHImin .lt. 0. .or. abs(PHImin) .lt. small) PHImin = -flag
2727       if (PHImin .gt. PI .or. abs(PHImin-PI) .lt. small) PHImin = PI
2728       if (PHImax .gt. PI .or. abs(PHImax-PI) .lt. small) PHImax = flag
2729       if (PHImax .lt. 0. .or. abs(PHImax) .lt. small) PHImax = 0.
2730       if (PHImax .lt. PHImin) PHImax = PHImin
2731 !     Calculate min and max angles coming from PHImin and PHImax,
2732 !     and put them in b_...
2733       call angles2tab(PHImin, PHImax, b_n, b_ang, b_tab)
2734 !     Construct the final table
2735       call construct_tab()
2736
2737       if (locmove_output) then
2738         print *,'FINAL TABLE'
2739         call output_tabs()
2740       endif
2741
2742 !     Check that there is at least one possible move
2743       no_moves = .true.
2744       if (res_n .eq. 0) then
2745         no_moves = .false.
2746       else
2747         index = 0
2748         do while ((index .lt. res_n) .and. no_moves)
2749           if (res_tab(2,1,index)) no_moves = .false.
2750           index=index+1
2751         enddo
2752       endif
2753
2754       if (no_moves) then
2755 !     Take care of the case where no solution exists...
2756         call fix_no_moves(phi)
2757         if (locmove_output) then
2758           print *,'   ***   Had to modify PHImin or PHImax'
2759           print *,'phi: ',phi*rad2deg
2760         endif
2761         move_res=1
2762       else
2763 !     ...or calculate the solution
2764 !     Construct phi_start/phi_end arrays
2765         call construct_ranges(phi_n, phi_start, phi_end)
2766 !     Choose random angle phi in allowed range(s)
2767         temp = 0.
2768         do i=0,phi_n-1
2769           temp = temp + phi_end(i) - phi_start(i)
2770         enddo
2771         phi = ran_number(phi_start(0),phi_start(0)+temp)
2772         index = 0
2773         done = .false.
2774         do while (.not.done)
2775           if (phi .lt. phi_end(index)) then
2776             done = .true.
2777           else
2778             index=index+1
2779           endif
2780           if (index .eq. phi_n) then
2781             done = .true.
2782           else if (.not.done) then
2783             phi = phi + phi_start(index) - phi_end(index-1)
2784           endif
2785         enddo
2786         if (index.eq.phi_n) phi=phi_end(phi_n-1) ! Fix numerical errors
2787         if (phi .gt. PI) phi = phi-2.*PI
2788
2789         if (locmove_output) then
2790           print *,'ALLOWED RANGE(S)'
2791           do i=0,phi_n-1
2792             print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2793           enddo
2794           print *,'phi: ',phi*rad2deg
2795         endif
2796         move_res=0
2797       endif
2798
2799 !     Re-use radius as temp variable
2800       temp=radius*cos(phi)
2801       radius=radius*sin(phi)
2802       do i=0,2
2803         c(i+1,i_move)=Orig(i)+temp*X(i)+radius*Y(i)
2804       enddo
2805
2806       return
2807       end function move_res
2808 !-----------------------------------------------------------------------------
2809       subroutine loc_test
2810 !rc      implicit none
2811
2812 !     Includes
2813 !      implicit real*8 (a-h,o-z)
2814 !      include 'DIMENSIONS'
2815 !      include 'COMMON.GEO'
2816 !      include 'COMMON.LOCAL'
2817 !      include 'COMMON.LOCMOVE'
2818
2819 !     External functions
2820 !EL      integer move_res
2821 !EL      external move_res
2822
2823 !     Local variables
2824       integer :: i,j,imov
2825       integer :: phi_n
2826       real(kind=8),dimension(0:11) :: phi_start,phi_end
2827       real(kind=8) :: phi
2828       real(kind=8),dimension(0:2,0:5) :: R
2829
2830       locmove_output=.true.
2831
2832 !      call angles2tab(30.*deg2rad,70.*deg2rad,a_n,a_ang,a_tab)
2833 !      call angles2tab(80.*deg2rad,130.*deg2rad,b_n,b_ang,b_tab)
2834 !      call minmax_angles(0.D0,3.8D0,0.D0,3.8D0,b_n,b_ang,b_tab)
2835 !      call construct_tab
2836 !      call output_tabs
2837
2838 !      call construct_ranges(phi_n,phi_start,phi_end)
2839 !      do i=0,phi_n-1
2840 !        print *,phi_start(i)*rad2deg,phi_end(i)*rad2deg
2841 !      enddo
2842
2843 !      call fix_no_moves(phi)
2844 !      print *,'NO MOVES FOUND, BEST PHI IS',phi*rad2deg
2845
2846       R(0,0)=0.D0
2847       R(1,0)=0.D0
2848       R(2,0)=0.D0
2849       R(0,1)=0.D0
2850       R(1,1)=-cos(28.D0*deg2rad)
2851       R(2,1)=-0.5D0-sin(28.D0*deg2rad)
2852       R(0,2)=0.D0
2853       R(1,2)=0.D0
2854       R(2,2)=-0.5D0
2855       R(0,3)=cos(30.D0*deg2rad)
2856       R(1,3)=0.D0
2857       R(2,3)=0.D0
2858       R(0,4)=0.D0
2859       R(1,4)=0.D0
2860       R(2,4)=0.5D0
2861       R(0,5)=0.D0
2862       R(1,5)=cos(26.D0*deg2rad)
2863       R(2,5)=0.5D0+sin(26.D0*deg2rad)
2864       do i=1,5
2865         do j=0,2
2866           R(j,i)=vbl*R(j,i)
2867         enddo
2868       enddo
2869 !      i=move_res(R(0,1),0.D0*deg2rad,180.D0*deg2rad)
2870       imov=2
2871       i=move_res(0.D0*deg2rad,180.D0*deg2rad,imov)
2872       print *,'RETURNED ',i
2873       print *,(R(i,3)/vbl,i=0,2)
2874
2875       return
2876       end subroutine loc_test
2877 #endif
2878 !-----------------------------------------------------------------------------
2879 ! matmult.f
2880 !-----------------------------------------------------------------------------
2881       subroutine MATMULT(A1,A2,A3)
2882 !      implicit real*8 (a-h,o-z)
2883 !      include 'DIMENSIONS'
2884 !el local variables
2885       integer :: i,j,k
2886       real(kind=8) :: A3IJ
2887
2888       real(kind=8),DIMENSION(3,3) :: A1,A2,A3
2889       real(kind=8),DIMENSION(3,3) :: AI3
2890       DO 1 I=1,3
2891         DO 2 J=1,3
2892           A3IJ=0.0
2893           DO 3 K=1,3
2894     3       A3IJ=A3IJ+A1(I,K)*A2(K,J)
2895           AI3(I,J)=A3IJ
2896     2   CONTINUE
2897     1 CONTINUE
2898       DO 4 I=1,3
2899       DO 4 J=1,3
2900     4   A3(I,J)=AI3(I,J)
2901       return
2902       end subroutine MATMULT
2903 !-----------------------------------------------------------------------------
2904 ! readpdb.F
2905 !-----------------------------------------------------------------------------
2906       subroutine int_from_cart(lside,lprn)
2907 !      implicit real*8 (a-h,o-z)
2908 !      include 'DIMENSIONS'
2909       use control_data,only:out1file
2910 #ifdef MPI
2911       include "mpif.h"
2912 #endif
2913 !      include 'COMMON.LOCAL'
2914 !      include 'COMMON.VAR'
2915 !      include 'COMMON.CHAIN'
2916 !      include 'COMMON.INTERACT'
2917 !      include 'COMMON.IOUNITS'
2918 !      include 'COMMON.GEO'
2919 !      include 'COMMON.NAMES'
2920 !      include 'COMMON.CONTROL'
2921 !      include 'COMMON.SETUP'
2922       character(len=3) :: seq,res
2923 !      character*5 atom
2924       character(len=80) :: card
2925       real(kind=8),dimension(3,20) :: sccor
2926       integer :: i,j,iti !el  rescode,
2927       logical :: lside,lprn
2928       real(kind=8) :: di,cosfac,sinfac
2929       integer :: nres2
2930       nres2=2*nres
2931
2932       if(me.eq.king.or..not.out1file)then
2933        if (lprn) then
2934         write (iout,'(/a)') &
2935         'Internal coordinates calculated from crystal structure.'
2936         if (lside) then
2937           write (iout,'(8a)') '  Res  ','       dvb','     Theta',&
2938        '     Gamma','    Dsc_id','       Dsc','     Alpha',&
2939        '     Beta '
2940         else
2941           write (iout,'(4a)') '  Res  ','       dvb','     Theta',&
2942        '     Gamma'
2943         endif
2944        endif
2945       endif
2946       do i=1,nres-1
2947 !       if (molnum(i).ne.1) cycle
2948 !in wham      do i=1,nres
2949         iti=itype(i,1)
2950         if (((dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0).and.&
2951        (iti.ne.ntyp1  .and. itype(i+1,1).ne.ntyp1)).and.molnum(i).eq.1) then
2952           write (iout,'(a,i4)') 'Bad Cartesians for residue',i
2953 !test          stop
2954         endif
2955 !#ifndef WHAM_RUN
2956         vbld(i+1)=dist(i,i+1)
2957         vbld_inv(i+1)=1.0d0/vbld(i+1)
2958 !#endif
2959         if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
2960         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
2961       enddo
2962 !el -----
2963 !#ifdef WHAM_RUN
2964 !      if (itype(1,1).eq.ntyp1) then
2965 !        do j=1,3
2966 !          c(j,1)=c(j,2)+(c(j,3)-c(j,4))
2967 !        enddo
2968 !      endif
2969 !      if (itype(nres,1).eq.ntyp1) then
2970 !        do j=1,3
2971 !          c(j,nres)=c(j,nres-1)+(c(j,nres-2)-c(j,nres-3))
2972 !        enddo
2973 !      endif
2974 !#endif
2975 !      if (unres_pdb) then
2976 !        if (itype(1,1).eq.21) then
2977 !          theta(3)=90.0d0*deg2rad
2978 !          phi(4)=180.0d0*deg2rad
2979 !          vbld(2)=3.8d0
2980 !          vbld_inv(2)=1.0d0/vbld(2)
2981 !        endif
2982 !        if (itype(nres,1).eq.21) then
2983 !          theta(nres)=90.0d0*deg2rad
2984 !          phi(nres)=180.0d0*deg2rad
2985 !          vbld(nres)=3.8d0
2986 !          vbld_inv(nres)=1.0d0/vbld(2)
2987 !        endif
2988 !      endif
2989       if (lside) then
2990         do i=2,nres-1
2991           do j=1,3
2992             c(j,nres2+2)=0.5D0*(2*c(j,i)+(c(j,i-1)-c(j,i))*vbld_inv(i) &
2993            +(c(j,i+1)-c(j,i))*vbld_inv(i+1))
2994 ! in wham            c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1)
2995           enddo
2996           iti=itype(i,1)
2997           di=dist(i,nres+i)
2998 !#ifndef WHAM_RUN
2999 ! 10/03/12 Adam: Correction for zero SC-SC bond length
3000
3001           if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1 .and. di.eq.0.0d0) &
3002            di=dsc(itype(i,molnum(i)))
3003           vbld(i+nres)=di
3004           if (itype(i,1).ne.10) then
3005             vbld_inv(i+nres)=1.0d0/di
3006           else
3007             vbld_inv(i+nres)=0.0d0
3008           endif
3009 !#endif
3010           if (iti.ne.10) then
3011             alph(i)=alpha(nres+i,i,nres2+2)
3012             omeg(i)=beta(nres+i,i,nres2+2,i+1)
3013           endif
3014           if (iti.ne.0) then
3015           if(me.eq.king.or..not.out1file)then
3016            if (lprn) &
3017            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3018            rad2deg*theta(i),rad2deg*phi(i),dsc(iti),vbld(nres+i),&
3019            rad2deg*alph(i),rad2deg*omeg(i)
3020           endif
3021           else
3022           if(me.eq.king.or..not.out1file)then
3023            if (lprn) &
3024            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,vbld(i),&
3025            rad2deg*theta(i),rad2deg*phi(i),dsc(iti+1),vbld(nres+i),&
3026            rad2deg*alph(i),rad2deg*omeg(i)
3027           endif
3028           endif
3029         enddo
3030       else if (lprn) then
3031         do i=2,nres
3032           iti=itype(i,1)
3033           if(me.eq.king.or..not.out1file) &
3034            write (iout,'(a3,i4,7f10.3)') restyp(iti,1),i,dist(i,i-1),&
3035            rad2deg*theta(i),rad2deg*phi(i)
3036         enddo
3037       endif
3038       return
3039       end subroutine int_from_cart
3040 !-----------------------------------------------------------------------------
3041       subroutine sc_loc_geom(lprn)
3042 !      implicit real*8 (a-h,o-z)
3043 !      include 'DIMENSIONS'
3044       use control_data,only:out1file
3045 #ifdef MPI
3046       include "mpif.h"
3047 #endif
3048 !      include 'COMMON.LOCAL'
3049 !      include 'COMMON.VAR'
3050 !      include 'COMMON.CHAIN'
3051 !      include 'COMMON.INTERACT'
3052 !      include 'COMMON.IOUNITS'
3053 !      include 'COMMON.GEO'
3054 !      include 'COMMON.NAMES'
3055 !      include 'COMMON.CONTROL'
3056 !      include 'COMMON.SETUP'
3057       real(kind=8),dimension(3) :: x_prime,y_prime,z_prime
3058       logical :: lprn
3059 !el local variables
3060       integer :: i,j,it,iti
3061       real(kind=8) :: cosfac2,sinfac2,xx,yy,zz,cosfac,sinfac
3062       do i=1,nres-1
3063         do j=1,3
3064           dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
3065         enddo
3066       enddo
3067       do i=2,nres-1
3068         if (itype(i,1).ne.10) then
3069           do j=1,3
3070             dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
3071           enddo
3072         else
3073           do j=1,3
3074             dc_norm(j,i+nres)=0.0d0
3075           enddo
3076         endif
3077       enddo
3078       do i=2,nres-1
3079         costtab(i+1) =dcos(theta(i+1))
3080         sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
3081         cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
3082         sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
3083         cosfac2=0.5d0/(1.0d0+costtab(i+1))
3084         cosfac=dsqrt(cosfac2)
3085         sinfac2=0.5d0/(1.0d0-costtab(i+1))
3086         sinfac=dsqrt(sinfac2)
3087         it=itype(i,1)
3088
3089         if ((it.ne.10).and.(it.ne.ntyp1)) then
3090 !el        if (it.ne.10) then
3091 !
3092 !  Compute the axes of tghe local cartesian coordinates system; store in
3093 !   x_prime, y_prime and z_prime
3094 !
3095         do j=1,3
3096           x_prime(j) = 0.00
3097           y_prime(j) = 0.00
3098           z_prime(j) = 0.00
3099         enddo
3100         do j = 1,3
3101           x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
3102           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
3103         enddo
3104         call vecpr(x_prime,y_prime,z_prime)
3105 !
3106 ! Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
3107 ! to local coordinate system. Store in xx, yy, zz.
3108 !
3109         xx=0.0d0
3110         yy=0.0d0
3111         zz=0.0d0
3112         do j = 1,3
3113           xx = xx + x_prime(j)*dc_norm(j,i+nres)
3114           yy = yy + y_prime(j)*dc_norm(j,i+nres)
3115           zz = zz + z_prime(j)*dc_norm(j,i+nres)
3116         enddo
3117
3118         xxref(i)=xx
3119         yyref(i)=yy
3120         zzref(i)=zz
3121         else
3122         xxref(i)=0.0d0
3123         yyref(i)=0.0d0
3124         zzref(i)=0.0d0
3125         endif
3126       enddo
3127       if (lprn) then
3128         do i=2,nres
3129           iti=itype(i,1)
3130           if(me.eq.king.or..not.out1file) &
3131            write (iout,'(a3,i4,3f10.5)') restyp(iti,1),i,xxref(i),&
3132             yyref(i),zzref(i)
3133         enddo
3134       endif
3135
3136       return
3137       end subroutine sc_loc_geom
3138 !-----------------------------------------------------------------------------
3139       subroutine sccenter(ires,nscat,sccor)
3140 !      implicit real*8 (a-h,o-z)
3141 !      include 'DIMENSIONS'
3142 !      include 'COMMON.CHAIN'
3143       integer :: i,j,ires,nscat
3144       real(kind=8),dimension(3,20) :: sccor
3145       real(kind=8) :: sccmj
3146 !        print *,"I am in sccenter",ires,nscat
3147       do j=1,3
3148         sccmj=0.0D0
3149         do i=1,nscat
3150           sccmj=sccmj+sccor(j,i)
3151 !C          print *,"insccent", ires,sccor(j,i)
3152         enddo
3153         dc(j,ires)=sccmj/nscat
3154       enddo
3155       return
3156       end subroutine sccenter
3157 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3158 !-----------------------------------------------------------------------------
3159       subroutine bond_regular
3160       use calc_data
3161 !      implicit real*8 (a-h,o-z)
3162 !      include 'DIMENSIONS'
3163 !      include 'COMMON.VAR'
3164 !      include 'COMMON.LOCAL'
3165 !      include 'COMMON.CALC'
3166 !      include 'COMMON.INTERACT'
3167 !      include 'COMMON.CHAIN'
3168       do i=1,nres-1
3169
3170        vbld(i+1)=vbl
3171        vbld_inv(i+1)=1.0d0/vbld(i+1)
3172        vbld(i+1+nres)=dsc(itype(i+1,molnum(i)))
3173        vbld_inv(i+1+nres)=dsc_inv(itype(i+1,molnum(i)))
3174 !       print *,vbld(i+1),vbld(i+1+nres)
3175       enddo
3176       return
3177       end subroutine bond_regular
3178 #endif
3179 !-----------------------------------------------------------------------------
3180 ! refsys.f
3181 !-----------------------------------------------------------------------------
3182       subroutine refsys(i2,i3,i4,e1,e2,e3,fail)
3183 ! This subroutine calculates unit vectors of a local reference system
3184 ! defined by atoms (i2), (i3), and (i4). The x axis is the axis from
3185 ! atom (i3) to atom (i2), and the xy plane is the plane defined by atoms
3186 ! (i2), (i3), and (i4). z axis is directed according to the sign of the
3187 ! vector product (i3)-(i2) and (i3)-(i4). Sets fail to .true. if atoms
3188 ! (i2) and (i3) or (i3) and (i4) coincide or atoms (i2), (i3), and (i4)
3189 ! form a linear fragment. Returns vectors e1, e2, and e3.
3190 !      implicit real*8 (a-h,o-z)
3191 !      include 'DIMENSIONS'
3192       logical :: fail
3193       real(kind=8),dimension(3) :: e1,e2,e3
3194       real(kind=8),dimension(3) :: u,z
3195 !      include 'COMMON.IOUNITS'
3196 !      include 'COMMON.CHAIN'
3197       real(kind=8) :: coinc=1.0D-13,align=1.0D-13
3198 !el local variables
3199       integer :: i,i1,i2,i3,i4
3200       real(kind=8) :: v1,v2,v3,s1,s2,zi,ui,anorm
3201       fail=.false.
3202       s1=0.0
3203       s2=0.0
3204       do 1 i=1,3
3205       zi=c(i,i2)-c(i,i3)
3206       ui=c(i,i4)-c(i,i3)
3207       s1=s1+zi*zi
3208       s2=s2+ui*ui
3209       z(i)=zi
3210     1 u(i)=ui
3211       s1=sqrt(s1)
3212       s2=sqrt(s2)
3213       if (s1.gt.coinc) goto 2
3214       write (iout,1000) i2,i3,i1
3215       fail=.true.
3216 !     do 3 i=1,3
3217 !   3 c(i,i1)=0.0D0
3218       return
3219     2 if (s2.gt.coinc) goto 4
3220       write(iout,1000) i3,i4,i1
3221       fail=.true.
3222       do 5 i=1,3
3223     5 c(i,i1)=0.0D0
3224       return
3225     4 s1=1.0/s1
3226       s2=1.0/s2
3227       v1=z(2)*u(3)-z(3)*u(2)
3228       v2=z(3)*u(1)-z(1)*u(3)
3229       v3=z(1)*u(2)-z(2)*u(1)
3230       anorm=dsqrt(v1*v1+v2*v2+v3*v3)
3231       if (anorm.gt.align) goto 6
3232       write (iout,1010) i2,i3,i4,i1
3233       fail=.true.
3234 !     do 7 i=1,3
3235 !   7 c(i,i1)=0.0D0
3236       return
3237     6 anorm=1.0D0/anorm
3238       e3(1)=v1*anorm
3239       e3(2)=v2*anorm
3240       e3(3)=v3*anorm
3241       e1(1)=z(1)*s1
3242       e1(2)=z(2)*s1
3243       e1(3)=z(3)*s1
3244       e2(1)=e1(3)*e3(2)-e1(2)*e3(3)
3245       e2(2)=e1(1)*e3(3)-e1(3)*e3(1)
3246       e2(3)=e1(2)*e3(1)-e1(1)*e3(2)
3247  1000 format (/1x,' * * * Error - atoms',i4,' and',i4,' coincide.',&
3248        'coordinates of atom',i4,' are set to zero.')
3249  1010 format (/1x,' * * * Error - atoms',2(i4,2h, ),i4,' form a linear',&
3250        ' fragment. coordinates of atom',i4,' are set to zero.')
3251       return
3252       end subroutine refsys
3253 !-----------------------------------------------------------------------------
3254 ! int_to_cart.f
3255 !-----------------------------------------------------------------------------
3256       subroutine int_to_cart
3257 !--------------------------------------------------------------
3258 !  This subroutine converts the energy derivatives from internal
3259 !  coordinates to cartesian coordinates
3260 !-------------------------------------------------------------
3261 !      implicit real*8 (a-h,o-z)
3262 !      include 'DIMENSIONS'
3263 !      include 'COMMON.VAR'
3264 !      include 'COMMON.CHAIN'
3265 !      include 'COMMON.DERIV'
3266 !      include 'COMMON.GEO'
3267 !      include 'COMMON.LOCAL'
3268 !      include 'COMMON.INTERACT'
3269 !      include 'COMMON.MD'
3270 !      include 'COMMON.IOUNITS'
3271 !      include 'COMMON.SCCOR'
3272 !   calculating dE/ddc1
3273 !el local variables
3274        integer :: j,i
3275 !       print *,"gloc",gloc(:,:)
3276 !       print *, "gcart",gcart(:,:)
3277        if (nres.lt.3) go to 18
3278        do j=1,3
3279          gcart(j,1)=gcart(j,1)+gloc(1,icg)*dphi(j,1,4) &
3280            +gloc(nres-2,icg)*dtheta(j,1,3)
3281           if ((itype(2,1).ne.10).and.&
3282           (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3283           gcart(j,1)=gcart(j,1)+gloc(ialph(2,1),icg)*dalpha(j,1,2)+ &
3284           gloc(ialph(2,1)+nside,icg)*domega(j,1,2)
3285         endif
3286        enddo
3287 !     Calculating the remainder of dE/ddc2
3288        do j=1,3
3289          gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ &
3290          gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4)
3291         if(itype(2,1).ne.10) then
3292           gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ &
3293           gloc(ialph(2,1)+nside,icg)*domega(j,2,2)
3294         endif
3295         if(itype(3,1).ne.10) then
3296           gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ &
3297           gloc(ialph(3,1)+nside,icg)*domega(j,1,3)
3298         endif
3299         if(nres.gt.4) then
3300           gcart(j,2)=gcart(j,2)+gloc(2,icg)*dphi(j,1,5)
3301         endif
3302        enddo
3303 !  If there are only five residues
3304        if(nres.eq.5) then
3305          do j=1,3
3306            gcart(j,3)=gcart(j,3)+gloc(1,icg)*dphi(j,3,4)+gloc(2,icg)* &
3307            dphi(j,2,5)+gloc(nres-1,icg)*dtheta(j,2,4)+gloc(nres,icg)* &
3308            dtheta(j,1,5)
3309 !         if(itype(3,1).ne.10) then
3310           if ((itype(3,1).ne.10).and.&
3311           (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) then
3312            gcart(j,3)=gcart(j,3)+gloc(ialph(3,1),icg)* &
3313            dalpha(j,2,3)+gloc(ialph(3,1)+nside,icg)*domega(j,2,3)
3314          endif
3315 !        if(itype(4,1).ne.10) then
3316           if ((itype(4,1).ne.10).and.&
3317           (itype(4,molnum(4)).ne.ntyp1_molec(molnum(4)))) then
3318            gcart(j,3)=gcart(j,3)+gloc(ialph(4,1),icg)* &
3319            dalpha(j,1,4)+gloc(ialph(4,1)+nside,icg)*domega(j,1,4)
3320          endif
3321         enddo
3322        endif
3323 !    If there are more than five residues
3324       if(nres.gt.5) then
3325         do i=3,nres-3
3326          do j=1,3
3327           gcart(j,i)=gcart(j,i)+gloc(i-2,icg)*dphi(j,3,i+1) &
3328           +gloc(i-1,icg)*dphi(j,2,i+2)+ &
3329           gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ &
3330           gloc(nres+i-3,icg)*dtheta(j,1,i+2)
3331           if(itype(i,1).ne.10) then
3332            gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ &
3333            gloc(ialph(i,1)+nside,icg)*domega(j,2,i)
3334           endif
3335           if(itype(i+1,1).ne.10) then
3336            gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) &
3337            +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1)
3338           endif
3339          enddo
3340         enddo
3341       endif
3342 !  Setting dE/ddnres-2
3343       if(nres.gt.5) then
3344          do j=1,3
3345            gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* &
3346            dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) &
3347            +gloc(2*nres-6,icg)* &
3348            dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres)
3349           if(itype(nres-2,1).ne.10) then
3350               gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* &
3351               dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* &
3352               domega(j,2,nres-2)
3353           endif
3354           if(itype(nres-1,1).ne.10) then
3355              gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* &
3356              dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3357              domega(j,1,nres-1)
3358           endif
3359          enddo
3360       endif
3361 !  Settind dE/ddnres-1
3362 !#define DEBUG
3363 #ifdef DEBUG
3364           j=1
3365               write(iout,*)"in int to carta",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
3371        do j=1,3
3372         gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ &
3373         gloc(2*nres-5,icg)*dtheta(j,2,nres)
3374 !#define DEBUG
3375 #ifdef DEBUG
3376               write(iout,*)"in int to cartb",nres-1,gcart(j,nres-1),gloc(nres-3,icg),dphi(j,3,nres), &
3377         gloc(2*nres-5,icg),dtheta(j,2,nres)
3378
3379 #endif
3380 !#undef DEBUG
3381         if(itype(nres-1,1).ne.10) then
3382           gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* &
3383           dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* &
3384           domega(j,2,nres-1)
3385 !#define DEBUG
3386 #ifdef DEBUG
3387               write(iout,*)"in int to cart2",i,gcart(j,nres-1),gloc(ialph(nres-1,1),icg)* &
3388           dalpha(j,2,nres-1),gloc(ialph(nres-1,1)+nside,icg), &
3389           domega(j,2,nres-1)
3390
3391 #endif
3392 !#undef DEBUG
3393
3394         endif
3395         enddo
3396 !   The side-chain vector derivatives
3397         do i=2,nres-1
3398          if(itype(i,1).ne.10 .and.  &
3399            itype(i,molnum(i)).ne.ntyp1_molec(molnum(i))) then
3400             do j=1,3
3401               gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) &
3402               +gloc(ialph(i,1)+nside,icg)*domega(j,3,i)
3403 !#define DEBUG
3404 #ifdef DEBUG
3405               write(iout,*)"in int to cart",i, gxcart(j,i),gloc(ialph(i,1),icg),dalpha(j,3,i), &
3406               gloc(ialph(i,1)+nside,icg),domega(j,3,i)
3407 #endif
3408 !#undef DEBUG
3409             enddo
3410          endif
3411        enddo
3412 !----------------------------------------------------------------------
3413 ! INTERTYP=1 SC...Ca...Ca...Ca
3414 ! INTERTYP=2 Ca...Ca...Ca...SC
3415 ! INTERTYP=3 SC...Ca...Ca...SC
3416 !   calculating dE/ddc1
3417   18   continue
3418 !       do i=1,nres
3419 !       gloc(i,icg)=0.0D0
3420 !          write (iout,*) "poczotkoawy",i,gloc_sc(1,i,icg)
3421 !       enddo
3422        if (nres.lt.2) return
3423        if ((nres.lt.3).and.(itype(1,1).eq.10)) return
3424        if ((itype(1,1).ne.10).and. &
3425         (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3426         do j=1,3
3427 !c Derviative was calculated for oposite vector of side chain therefore
3428 ! there is "-" sign before gloc_sc
3429          gxcart(j,1)=gxcart(j,1)-gloc_sc(1,0,icg)* &
3430            dtauangle(j,1,1,3)
3431          gcart(j,1)=gcart(j,1)+gloc_sc(1,0,icg)* &
3432            dtauangle(j,1,2,3)
3433           if ((itype(2,1).ne.10).and. &
3434         (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) then
3435          gxcart(j,1)= gxcart(j,1) &
3436                      -gloc_sc(3,0,icg)*dtauangle(j,3,1,3)
3437          gcart(j,1)=gcart(j,1)+gloc_sc(3,0,icg)* &
3438             dtauangle(j,3,2,3)
3439           endif
3440        enddo
3441        endif
3442          if ((nres.ge.3).and.(itype(3,molnum(3)).ne.10).and.&
3443          (itype(3,molnum(3)).ne.ntyp1_molec(molnum(3)))) &
3444       then
3445          do j=1,3
3446          gcart(j,1)=gcart(j,1)+gloc_sc(2,1,icg)*dtauangle(j,2,1,4)
3447          enddo
3448          endif
3449 !   As potetnial DO NOT depend on omicron anlge their derivative is
3450 !   ommited
3451 !     &     +gloc_sc(intertyp,nres-2,icg)*dtheta(j,1,3)
3452
3453 !     Calculating the remainder of dE/ddc2
3454        do j=1,3
3455          if((itype(2,1).ne.10).and. &
3456            (itype(2,molnum(2)).ne.ntyp1_molec(molnum(2)))) 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)+ &
3460                                gloc_sc(3,0,icg)*dtauangle(j,3,3,3)
3461         if ((itype(3,1).ne.10).and.(nres.ge.3).and.(itype(3,molnum(3)).ne.ntyp1_molec(3))) &
3462          then
3463            gxcart(j,2)=gxcart(j,2)-gloc_sc(3,1,icg)*dtauangle(j,3,1,4)
3464 !c                  the   - above is due to different vector direction
3465            gcart(j,2)=gcart(j,2)+gloc_sc(3,1,icg)*dtauangle(j,3,2,4)
3466           endif
3467           if (nres.gt.3) then
3468 !           if ((itype(1,1).ne.10).and.&
3469 !              ((itype(1,molnum(1)).ne.ntyp1_molec(molnum(1))))) &
3470            gxcart(j,2)=gxcart(j,2)-gloc_sc(1,1,icg)*dtauangle(j,1,1,4)
3471 !c                  the   - above is due to different vector direction
3472            gcart(j,2)=gcart(j,2)+gloc_sc(1,1,icg)*dtauangle(j,1,2,4)
3473 !          write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,2,4),"gcart"
3474 !           write(iout,*) gloc_sc(1,1,icg),dtauangle(j,1,1,4),"gx"
3475           endif
3476          endif
3477          if ((itype(1,1).ne.10).and.&
3478          (itype(1,molnum(1)).ne.ntyp1_molec(molnum(1)))) then
3479           gcart(j,2)=gcart(j,2)+gloc_sc(1,0,icg)*dtauangle(j,1,3,3)
3480 !           write(iout,*)  gloc_sc(1,0,icg),dtauangle(j,1,3,3)
3481         endif
3482          if ((itype(3,1).ne.10).and.(nres.ge.3)) then
3483           gcart(j,2)=gcart(j,2)+gloc_sc(2,1,icg)*dtauangle(j,2,2,4)
3484 !           write(iout,*) gloc_sc(2,1,icg),dtauangle(j,2,2,4)
3485          endif
3486          if ((itype(4,1).ne.10).and.(nres.ge.4)) then
3487           gcart(j,2)=gcart(j,2)+gloc_sc(2,2,icg)*dtauangle(j,2,1,5)
3488 !           write(iout,*) gloc_sc(2,2,icg),dtauangle(j,2,1,5)
3489          endif
3490
3491 !      write(iout,*) gcart(j,2),itype(2,1),itype(1,1),itype(3,1), "gcart2"
3492        enddo
3493 !    If there are more than five residues
3494       if(nres.ge.5) then
3495         do i=3,nres-2
3496          do j=1,3
3497 !          write(iout,*) "before", gcart(j,i)
3498           if ((itype(i,1).ne.10).and.&
3499           (itype(i,molnum(i)).ne.ntyp1_molec(molnum(i)))) then
3500           gxcart(j,i)=gxcart(j,i)+gloc_sc(2,i-2,icg) &
3501           *dtauangle(j,2,3,i+1) &
3502           -gloc_sc(1,i-1,icg)*dtauangle(j,1,1,i+2)
3503           gcart(j,i)=gcart(j,i)+gloc_sc(1,i-1,icg) &
3504           *dtauangle(j,1,2,i+2)
3505 !                   write(iout,*) "new",j,i,
3506 !     &  gcart(j,i),gloc_sc(1,i-1,icg),dtauangle(j,1,2,i+2)
3507 !          if (itype(i-1,1).ne.10) then
3508           if ((itype(i-1,1).ne.10).and.&
3509           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3510
3511            gxcart(j,i)=gxcart(j,i)+gloc_sc(3,i-2,icg) &
3512       *dtauangle(j,3,3,i+1)
3513           endif
3514 !          if (itype(i+1,1).ne.10) then
3515           if ((itype(i+1,1).ne.10).and.&
3516           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3517           gxcart(j,i)=gxcart(j,i)-gloc_sc(3,i-1,icg) &
3518       *dtauangle(j,3,1,i+2)
3519            gcart(j,i)=gcart(j,i)+gloc_sc(3,i-1,icg) &
3520       *dtauangle(j,3,2,i+2)
3521           endif
3522           endif
3523 !          if (itype(i-1,1).ne.10) then
3524           if ((itype(i-1,1).ne.10).and.&
3525           (itype(i-1,molnum(i-1)).ne.ntyp1_molec(molnum(i-1)))) then
3526            gcart(j,i)=gcart(j,i)+gloc_sc(1,i-2,icg)* &
3527            dtauangle(j,1,3,i+1)
3528           endif
3529 !          if (itype(i+1,1).ne.10) then
3530           if ((itype(i+1,1).ne.10).and.&
3531           (itype(i+1,molnum(i+1)).ne.ntyp1_molec(molnum(i+1)))) then
3532            gcart(j,i)=gcart(j,i)+gloc_sc(2,i-1,icg)* &
3533            dtauangle(j,2,2,i+2)
3534 !          write(iout,*) "numer",i,gloc_sc(2,i-1,icg),
3535 !     &    dtauangle(j,2,2,i+2)
3536           endif
3537 !          if (itype(i+2,1).ne.10) then
3538           if ((itype(i+2,1).ne.10).and.&
3539           (itype(i+2,molnum(i+2)).ne.ntyp1_molec(molnum(i+2)))) then
3540            gcart(j,i)=gcart(j,i)+gloc_sc(2,i,icg)* &
3541            dtauangle(j,2,1,i+3)
3542           endif
3543          enddo
3544         enddo
3545       endif
3546 !  Setting dE/ddnres-1
3547       if(nres.ge.4) then
3548          do j=1,3
3549          if ((itype(nres-1,1).ne.10).and.&
3550        (itype(nres-1,molnum(nres-1)).ne.ntyp1_molec(molnum(nres-1)))) then
3551          gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(2,nres-3,icg) &
3552           *dtauangle(j,2,3,nres)
3553 !          write (iout,*) "gxcart(nres-1)", gloc_sc(2,nres-3,icg),
3554 !     &     dtauangle(j,2,3,nres), gxcart(j,nres-1)
3555 !         if (itype(nres-2,1).ne.10) then
3556          if ((itype(nres-2,1).ne.10).and.&
3557        (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3558        gxcart(j,nres-1)=gxcart(j,nres-1)+gloc_sc(3,nres-3,icg) &
3559           *dtauangle(j,3,3,nres)
3560           endif
3561          if ((itype(nres,1).ne.10).and.&
3562          (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3563         gxcart(j,nres-1)=gxcart(j,nres-1)-gloc_sc(3,nres-2,icg) &
3564           *dtauangle(j,3,1,nres+1)
3565         gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(3,nres-2,icg) &
3566           *dtauangle(j,3,2,nres+1)
3567           endif
3568          endif
3569          if ((itype(nres-2,1).ne.10).and.&
3570          (itype(nres-2,molnum(nres-2)).ne.ntyp1_molec(molnum(nres-2)))) then
3571             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(1,nres-3,icg)* &
3572          dtauangle(j,1,3,nres)
3573          endif
3574           if ((itype(nres,1).ne.10).and.(itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres)))) then
3575             gcart(j,nres-1)=gcart(j,nres-1)+gloc_sc(2,nres-2,icg)* &
3576            dtauangle(j,2,2,nres+1)
3577 !           write (iout,*) "gcart(nres-1)", gloc_sc(2,nres-2,icg),
3578 !     &     dtauangle(j,2,2,nres+1), itype(nres-1,1),itype(nres,1)
3579            endif
3580          enddo
3581       endif
3582 !  Settind dE/ddnres
3583        if ((nres.ge.3).and.(itype(nres,1).ne.10).and. &
3584           (itype(nres,molnum(nres)).ne.ntyp1_molec(molnum(nres))))then
3585        do j=1,3
3586         gxcart(j,nres)=gxcart(j,nres)+gloc_sc(3,nres-2,icg) &
3587        *dtauangle(j,3,3,nres+1)+gloc_sc(2,nres-2,icg) &
3588        *dtauangle(j,2,3,nres+1)
3589         enddo
3590        endif
3591 !   The side-chain vector derivatives
3592 !       print *,"gcart",gcart(:,:)
3593       return
3594       end subroutine int_to_cart
3595 #if .not. defined(WHAM_RUN) && .not. defined(CLUSTER)
3596 !-----------------------------------------------------------------------------
3597 ! readrtns_CSA.F
3598 !-----------------------------------------------------------------------------
3599       subroutine gen_dist_constr
3600 ! Generate CA distance constraints.
3601 !      implicit real*8 (a-h,o-z)
3602 !      include 'DIMENSIONS'
3603 !      include 'COMMON.IOUNITS'
3604 !      include 'COMMON.GEO'
3605 !      include 'COMMON.VAR'
3606 !      include 'COMMON.INTERACT'
3607 !      include 'COMMON.LOCAL'
3608 !      include 'COMMON.NAMES'
3609 !      include 'COMMON.CHAIN'
3610 !      include 'COMMON.FFIELD'
3611 !      include 'COMMON.SBRIDGE'
3612 !      include 'COMMON.HEADER'
3613 !      include 'COMMON.CONTROL'
3614 !      include 'COMMON.DBASE'
3615 !      include 'COMMON.THREAD'
3616 !      include 'COMMON.TIME1'
3617 !      integer :: itype_pdb !(maxres)
3618 !      common /pizda/ itype_pdb(nres)
3619       character(len=2) :: iden
3620 !el local variables
3621       integer :: i,j
3622 !d      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
3623 !d      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
3624 !d     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
3625 !d     & ' nsup',nsup
3626       do i=nstart_sup,nstart_sup+nsup-1
3627 !d      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
3628 !d     &    ' seq_pdb', restyp(itype_pdb(i))
3629         do j=i+2,nstart_sup+nsup-1
3630           nhpb=nhpb+1
3631           ihpb(nhpb)=i+nstart_seq-nstart_sup
3632           jhpb(nhpb)=j+nstart_seq-nstart_sup
3633           forcon(nhpb)=weidis
3634           dhpb(nhpb)=dist(i,j)
3635         enddo
3636       enddo
3637 !d      write (iout,'(a)') 'Distance constraints:'
3638 !d      do i=nss+1,nhpb
3639 !d        ii=ihpb(i)
3640 !d        jj=jhpb(i)
3641 !d        iden='CA'
3642 !d        if (ii.gt.nres) then
3643 !d          iden='SC'
3644 !d          ii=ii-nres
3645 !d          jj=jj-nres
3646 !d        endif
3647 !d        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
3648 !d     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
3649 !d     &  dhpb(i),forcon(i)
3650 !d      enddo
3651 !      deallocate(itype_pdb)
3652
3653       return
3654       end subroutine gen_dist_constr
3655 #endif
3656 !-----------------------------------------------------------------------------
3657 ! cartprint.f
3658 !-----------------------------------------------------------------------------
3659       subroutine cartprint
3660
3661       use geometry_data, only: c
3662       use energy_data, only: itype
3663 !      implicit real*8 (a-h,o-z)
3664 !      include 'DIMENSIONS'
3665 !      include 'COMMON.CHAIN'
3666 !      include 'COMMON.INTERACT'
3667 !      include 'COMMON.NAMES'
3668 !      include 'COMMON.IOUNITS'
3669       integer :: i
3670
3671       write (iout,100)
3672       do i=1,nres
3673         write (iout,110) restyp(itype(i,1),1),i,c(1,i),c(2,i),&
3674           c(3,i),c(1,nres+i),c(2,nres+i),c(3,nres+i)
3675       enddo
3676   100 format (//'              alpha-carbon coordinates       ',&
3677                 '     centroid coordinates'/ &
3678                 '       ', 6X,'X',11X,'Y',11X,'Z',&
3679                                 10X,'X',11X,'Y',11X,'Z')
3680   110 format (a,'(',i3,')',6f12.5)
3681       return
3682       end subroutine cartprint
3683 !-----------------------------------------------------------------------------
3684 !-----------------------------------------------------------------------------
3685       subroutine alloc_geo_arrays
3686 !EL Allocation of tables used by module energy
3687
3688       integer :: i,j,nres2
3689       nres2=2*nres
3690 ! commom.bounds
3691 !      common /bounds/
3692       allocate(phibound(2,nres+2)) !(2,maxres)
3693 !----------------------
3694 ! commom.chain
3695 !      common /chain/ in molread
3696 !      real(kind=8),dimension(:,:),allocatable :: c !(3,maxres2+2)
3697 !      real(kind=8),dimension(:,:),allocatable :: dc
3698       allocate(dc_old(3,0:nres2))
3699 !      if(.not.allocated(dc_norm2)) allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3700       if(.not.allocated(dc_norm2)) then
3701         allocate(dc_norm2(3,0:nres2+2)) !(3,0:maxres2)
3702         dc_norm2(:,:)=0.d0
3703       endif
3704 !
3705 !el      if(.not.allocated(dc_norm))
3706 !elwrite(iout,*) "jestem w alloc geo 1"
3707       if(.not.allocated(dc_norm)) then
3708         allocate(dc_norm(3,0:nres2+2)) !(3,0:maxres2)
3709         dc_norm(:,:)=0.d0
3710       endif
3711 !elwrite(iout,*) "jestem w alloc geo 1"
3712       allocate(xloc(3,nres),xrot(3,nres))
3713 !elwrite(iout,*) "jestem w alloc geo 1"
3714       xloc(:,:)=0.0D0
3715 !elwrite(iout,*) "jestem w alloc geo 1"
3716       allocate(dc_work(6*nres)) !(MAXRES6) maxres6=6*maxres
3717 !      common /rotmat/
3718       allocate(t(3,3,nres),r(3,3,nres))
3719       allocate(prod(3,3,nres),rt(3,3,nres)) !(3,3,maxres)
3720 !      common /refstruct/
3721       if(.not.allocated(cref)) allocate(cref(3,nres2+2,maxperm)) !(3,maxres2+2,maxperm)
3722 !elwrite(iout,*) "jestem w alloc geo 2"
3723       allocate(crefjlee(3,nres2+2)) !(3,maxres2+2)
3724       if(.not.allocated(chain_rep)) allocate(chain_rep(3,nres2+2,maxsym)) !(3,maxres2+2,maxsym)
3725       if(.not.allocated(tabperm)) allocate(tabperm(maxperm,maxsym)) !(maxperm,maxsym)
3726 !      common /from_zscore/ in module.compare
3727 !----------------------
3728 ! common.local
3729 ! Inverses of the actual virtual bond lengths
3730 !      common /invlen/ in io_conf: molread or readpdb
3731 !      real(kind=8),dimension(:),allocatable :: vbld_inv !(maxres2)
3732 !----------------------
3733 ! common.var
3734 ! Store the geometric variables in the following COMMON block.
3735 !      common /var/ in readpdb or ...
3736       if(.not.allocated(theta)) allocate(theta(nres+2))
3737       if(.not.allocated(phi)) allocate(phi(nres+2))
3738       if(.not.allocated(alph)) allocate(alph(nres+2))
3739       if(.not.allocated(omeg)) allocate(omeg(nres+2))
3740       if(.not.allocated(thetaref)) allocate(thetaref(nres+2))
3741       if(.not.allocated(phiref)) allocate(phiref(nres+2))
3742       if(.not.allocated(costtab)) allocate(costtab(nres))
3743       if(.not.allocated(sinttab)) allocate(sinttab(nres))
3744       if(.not.allocated(cost2tab)) allocate(cost2tab(nres))
3745       if(.not.allocated(sint2tab)) allocate(sint2tab(nres))
3746 !      real(kind=8),dimension(:),allocatable :: vbld !(2*maxres) in io_conf: molread or readpdb
3747       allocate(omicron(2,nres+2)) !(2,maxres)
3748       allocate(tauangle(3,nres+2)) !(3,maxres)
3749 !elwrite(iout,*) "jestem w alloc geo 3"
3750       if(.not.allocated(xxtab)) allocate(xxtab(nres))
3751       if(.not.allocated(yytab)) allocate(yytab(nres))
3752       if(.not.allocated(zztab)) allocate(zztab(nres)) !(maxres)
3753       if(.not.allocated(xxref)) allocate(xxref(nres))
3754       if(.not.allocated(yyref)) allocate(yyref(nres))
3755       if(.not.allocated(zzref)) allocate(zzref(nres)) !(maxres)
3756       allocate(ialph(nres,2)) !(maxres,2)
3757       ialph(:,1)=0
3758       ialph(:,2)=0
3759       allocate(ivar(4*nres2)) !(4*maxres2)
3760
3761 #if defined(WHAM_RUN) || defined(CLUSTER)
3762       allocate(vbld(2*nres))
3763       vbld(:)=0.d0
3764       allocate(vbld_inv(2*nres))
3765       vbld_inv(:)=0.d0
3766 #endif
3767
3768       return
3769       end subroutine alloc_geo_arrays
3770 !-----------------------------------------------------------------------------
3771 !-----------------------------------------------------------------------------
3772       subroutine returnbox
3773       integer :: allareout,i,j,k,nojumpval,chain_beg,mnum
3774       integer :: chain_end,ireturnval
3775       real*8 :: difference
3776 !C change suggested by Ana - end
3777         j=1
3778         chain_beg=1
3779 !C        do i=1,nres
3780 !C       write(*,*) 'initial', i,j,c(j,i)
3781 !C        enddo
3782 !C change suggested by Ana - begin
3783         allareout=1
3784 !C change suggested by Ana -end
3785         do i=1,nres-1
3786            mnum=molnum(i)
3787          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3788             .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3789           chain_end=i
3790           if (allareout.eq.1) then
3791             ireturnval=int(c(j,i)/boxxsize)
3792             if (c(j,i).le.0) ireturnval=ireturnval-1
3793             do k=chain_beg,chain_end
3794               c(j,k)=c(j,k)-ireturnval*boxxsize
3795               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3796             enddo
3797 !C Suggested by Ana
3798             if (chain_beg.eq.1) &
3799             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3800 !C Suggested by Ana -end
3801            endif
3802            chain_beg=i+1
3803            allareout=1
3804          else
3805           if (int(c(j,i)/boxxsize).eq.0) allareout=0
3806          endif
3807         enddo
3808          if (allareout.eq.1) then
3809             ireturnval=int(c(j,i)/boxxsize)
3810             if (c(j,i).le.0) ireturnval=ireturnval-1
3811             do k=chain_beg,nres
3812               c(j,k)=c(j,k)-ireturnval*boxxsize
3813               c(j,k+nres)=c(j,k+nres)-ireturnval*boxxsize
3814             enddo
3815           endif
3816 !C NO JUMP
3817 !C        do i=1,nres
3818 !C        write(*,*) 'befor no jump', i,j,c(j,i)
3819 !C        enddo
3820         nojumpval=0
3821         do i=2,nres
3822            mnum=molnum(i)
3823            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3824               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3825              difference=abs(c(j,i-1)-c(j,i))
3826 !C             print *,'diff', difference
3827              if (difference.gt.boxxsize/2.0) then
3828                 if (c(j,i-1).gt.c(j,i)) then
3829                   nojumpval=1
3830                  else
3831                    nojumpval=-1
3832                  endif
3833               else
3834               nojumpval=0
3835               endif
3836               endif
3837               c(j,i)=c(j,i)+nojumpval*boxxsize
3838               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3839          enddo
3840        nojumpval=0
3841         do i=2,nres
3842            mnum=molnum(i)
3843            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3844              difference=abs(c(j,i-1)-c(j,i))
3845              if (difference.gt.boxxsize/2.0) then
3846                 if (c(j,i-1).gt.c(j,i)) then
3847                   nojumpval=1
3848                  else
3849                    nojumpval=-1
3850                  endif
3851               else
3852               nojumpval=0
3853               endif
3854              endif
3855               c(j,i)=c(j,i)+nojumpval*boxxsize
3856               c(j,i+nres)=c(j,i+nres)+nojumpval*boxxsize
3857          enddo
3858
3859 !C        do i=1,nres
3860 !C        write(*,*) 'after no jump', i,j,c(j,i)
3861 !C        enddo
3862
3863 !C NOW Y dimension
3864 !C suggesed by Ana begins
3865         allareout=1
3866         j=2
3867         chain_beg=1
3868         do i=1,nres-1
3869            mnum=molnum(i)
3870          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3871            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3872           chain_end=i
3873           if (allareout.eq.1) then
3874             ireturnval=int(c(j,i)/boxysize)
3875             if (c(j,i).le.0) ireturnval=ireturnval-1
3876             do k=chain_beg,chain_end
3877               c(j,k)=c(j,k)-ireturnval*boxysize
3878              c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3879             enddo
3880 !C Suggested by Ana
3881             if (chain_beg.eq.1) &
3882             dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3883 !C Suggested by Ana -end
3884            endif
3885            chain_beg=i+1
3886            allareout=1
3887          else
3888           if (int(c(j,i)/boxysize).eq.0) allareout=0
3889          endif
3890         enddo
3891          if (allareout.eq.1) then
3892             ireturnval=int(c(j,i)/boxysize)
3893             if (c(j,i).le.0) ireturnval=ireturnval-1
3894             do k=chain_beg,nres
3895               c(j,k)=c(j,k)-ireturnval*boxysize
3896               c(j,k+nres)=c(j,k+nres)-ireturnval*boxysize
3897             enddo
3898           endif
3899         nojumpval=0
3900         do i=2,nres
3901            mnum=molnum(i)
3902            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3903               .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3904              difference=abs(c(j,i-1)-c(j,i))
3905              if (difference.gt.boxysize/2.0) then
3906                 if (c(j,i-1).gt.c(j,i)) then
3907                   nojumpval=1
3908                  else
3909                    nojumpval=-1
3910                  endif
3911              else
3912               nojumpval=0
3913               endif
3914            endif
3915               c(j,i)=c(j,i)+nojumpval*boxysize
3916               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3917          enddo
3918       nojumpval=0
3919         do i=2,nres
3920            mnum=molnum(i)
3921            if (itype(i,mnum).eq.ntyp1_molec(mnum)&
3922              .and. itype(i-1,mnum).eq.ntyp1) then
3923              difference=abs(c(j,i-1)-c(j,i))
3924              if (difference.gt.boxysize/2.0) then
3925                 if (c(j,i-1).gt.c(j,i)) then
3926                   nojumpval=1
3927                  else
3928                    nojumpval=-1
3929                  endif
3930               else
3931               nojumpval=0
3932               endif
3933             endif
3934               c(j,i)=c(j,i)+nojumpval*boxysize
3935               c(j,i+nres)=c(j,i+nres)+nojumpval*boxysize
3936          enddo
3937 !C Now Z dimension
3938 !C Suggested by Ana -begins
3939         allareout=1
3940 !C Suggested by Ana -ends
3941        j=3
3942         chain_beg=1
3943         do i=1,nres-1
3944            mnum=molnum(i)
3945          if ((itype(i,mnum).eq.ntyp1_molec(mnum))&
3946            .and.(itype(i+1,mnum).eq.ntyp1_molec(mnum))) then
3947           chain_end=i
3948           if (allareout.eq.1) then
3949             ireturnval=int(c(j,i)/boxysize)
3950             if (c(j,i).le.0) ireturnval=ireturnval-1
3951             do k=chain_beg,chain_end
3952               c(j,k)=c(j,k)-ireturnval*boxzsize
3953               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3954             enddo
3955 !C Suggested by Ana
3956             if (chain_beg.eq.1) dc_old(1,0)=dc_old(1,0)-ireturnval*boxxsize
3957 !C Suggested by Ana -end
3958            endif
3959            chain_beg=i+1
3960            allareout=1
3961          else
3962           if (int(c(j,i)/boxzsize).eq.0) allareout=0
3963          endif
3964         enddo
3965          if (allareout.eq.1) then
3966             ireturnval=int(c(j,i)/boxzsize)
3967             if (c(j,i).le.0) ireturnval=ireturnval-1
3968             do k=chain_beg,nres
3969               c(j,k)=c(j,k)-ireturnval*boxzsize
3970               c(j,k+nres)=c(j,k+nres)-ireturnval*boxzsize
3971             enddo
3972           endif
3973         nojumpval=0
3974         do i=2,nres
3975            mnum=molnum(i)
3976            if (itype(i,mnum).eq.ntyp1_molec(mnum) .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3977              difference=abs(c(j,i-1)-c(j,i))
3978              if (difference.gt.(boxzsize/2.0)) then
3979                 if (c(j,i-1).gt.c(j,i)) then
3980                   nojumpval=1
3981                  else
3982                    nojumpval=-1
3983                  endif
3984               else
3985               nojumpval=0
3986               endif
3987             endif
3988               c(j,i)=c(j,i)+nojumpval*boxzsize
3989               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
3990          enddo
3991        nojumpval=0
3992         do i=2,nres
3993            mnum=molnum(i)
3994            if (itype(i,mnum).eq.ntyp1_molec(mnum) &
3995             .and. itype(i-1,mnum).eq.ntyp1_molec(mnum)) then
3996              difference=abs(c(j,i-1)-c(j,i))
3997              if (difference.gt.boxzsize/2.0) then
3998                 if (c(j,i-1).gt.c(j,i)) then
3999                   nojumpval=1
4000                  else
4001                    nojumpval=-1
4002                  endif
4003               else
4004               nojumpval=0
4005               endif
4006             endif
4007              c(j,i)=c(j,i)+nojumpval*boxzsize
4008               c(j,i+nres)=c(j,i+nres)+nojumpval*boxzsize
4009          enddo
4010         do i=1,nres
4011          if (molnum(i).eq.5) then
4012           c(1,i)=dmod(c(1,i),boxxsize)
4013           c(2,i)=dmod(c(2,i),boxysize)
4014           c(3,i)=dmod(c(3,i),boxzsize)
4015           c(1,i+nres)=dmod(c(1,i+nres),boxxsize)
4016           c(2,i+nres)=dmod(c(2,i+nres),boxysize)
4017           c(3,i+nres)=dmod(c(3,i+nres),boxzsize)
4018          endif
4019         enddo
4020         return
4021         end       subroutine returnbox
4022 !-------------------------------------------------------------------------------------------------------
4023       end module geometry