source/unres/src_MD-M/readrtns_CSA.F

   1       subroutine readrtns
   2       implicit real*8 (a-h,o-z)
   3       include 'DIMENSIONS'
   4 #ifdef MPI
   5       include 'mpif.h'
   6 #endif
   7       include 'COMMON.SETUP'
   8       include 'COMMON.CONTROL'
   9       include 'COMMON.SBRIDGE'
  10       include 'COMMON.IOUNITS'
  11       logical file_exist
  12 C Read force-field parameters except weights
  13       call parmread
  14 C Read job setup parameters
  15       call read_control
  16 C Read control parameters for energy minimzation if required
  17       if (minim) call read_minim
  18 C Read MCM control parameters if required
  19       if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
  20 C Read MD control parameters if reqjuired
  21       if (modecalc.eq.12) call read_MDpar
  22 C Read MREMD control parameters if required
  23       if (modecalc.eq.14) then
  24          call read_MDpar
  25          call read_REMDpar
  26       endif
  27 C Read MUCA control parameters if required
  28       if (lmuca) call read_muca
  29 C Read CSA control parameters if required (from fort.40 if exists
  30 C otherwise from general input file)
  31       if (modecalc.eq.8) then
  32        inquire (file="fort.40",exist=file_exist)
  33        if (.not.file_exist) call csaread
  34       endif
  35 cfmc      if (modecalc.eq.10) call mcmfread
  36 C Read molecule information, molecule geometry, energy-term weights, and
  37 C restraints if requested
  38       call molread
  39 C Print restraint information
  40 #ifdef MPI
  41       if (.not. out1file .or. me.eq.king) then
  42 #endif
  43       if (nhpb.gt.nss)
  44      &write (iout,'(a,i5,a)') "The following",nhpb-nss,
  45      & " distance constraints have been imposed"
  46       do i=nss+1,nhpb
  47         write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
  48       enddo
  49 #ifdef MPI
  50       endif
  51 #endif
  52 c      print *,"Processor",myrank," leaves READRTNS"
  53       return
  54       end
  55 C-------------------------------------------------------------------------------
  56       subroutine read_control
  57 C
  58 C Read contorl data
  59 C
  60       implicit real*8 (a-h,o-z)
  61       include 'DIMENSIONS'
  62 #ifdef MP
  63       include 'mpif.h'
  64       logical OKRandom, prng_restart
  65       real*8  r1
  66 #endif
  67       include 'COMMON.IOUNITS'
  68       include 'COMMON.TIME1'
  69       include 'COMMON.THREAD'
  70       include 'COMMON.SBRIDGE'
  71       include 'COMMON.CONTROL'
  72       include 'COMMON.MCM'
  73       include 'COMMON.MAP'
  74       include 'COMMON.HEADER'
  75       include 'COMMON.CSA'
  76       include 'COMMON.CHAIN'
  77       include 'COMMON.MUCA'
  78       include 'COMMON.MD'
  79       include 'COMMON.FFIELD'
  80       include 'COMMON.INTERACT'
  81       include 'COMMON.SETUP'
  82       COMMON /MACHSW/ KDIAG,ICORFL,IXDR
  83       character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/
  84       character*80 ucase
  85       character*320 controlcard
  86
  87       nglob_csa=0
  88       eglob_csa=1d99
  89       nmin_csa=0
  90       read (INP,'(a)') titel
  91       call card_concat(controlcard)
  92 c      out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0
  93 c      print *,"Processor",me," fg_rank",fg_rank," out1file",out1file
  94       call reada(controlcard,'SEED',seed,0.0D0)
  95       call random_init(seed)
  96 C Set up the time limit (caution! The time must be input in minutes!)
  97       read_cart=index(controlcard,'READ_CART').gt.0
  98       call readi(controlcard,'CONSTR_DIST',constr_dist,0)
  99       call readi(controlcard,'SYM',symetr,1)
 100       call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
 101       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
 102       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
 103       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
 104       call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
 105       call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
 106       call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
 107       call reada(controlcard,'DRMS',drms,0.1D0)
 108       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
 109        write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
 110        write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
 111        write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
 112        write (iout,'(a,f10.1)')'DRMS    = ',drms
 113        write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
 114        write (iout,'(a,f10.1)') 'Time limit (min):',timlim
 115       endif
 116       call readi(controlcard,'NZ_START',nz_start,0)
 117       call readi(controlcard,'NZ_END',nz_end,0)
 118       call readi(controlcard,'IZ_SC',iz_sc,0)
 119       timlim=60.0D0*timlim
 120       safety = 60.0d0*safety
 121       timem=timlim
 122       modecalc=0
 123       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 124       minim=(index(controlcard,'MINIMIZE').gt.0)
 125       dccart=(index(controlcard,'CART').gt.0)
 126       overlapsc=(index(controlcard,'OVERLAP').gt.0)
 127       overlapsc=.not.overlapsc
 128       searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
 129       searchsc=.not.searchsc
 130       sideadd=(index(controlcard,'SIDEADD').gt.0)
 131       energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
 132       outpdb=(index(controlcard,'PDBOUT').gt.0)
 133       outmol2=(index(controlcard,'MOL2OUT').gt.0)
 134       pdbref=(index(controlcard,'PDBREF').gt.0)
 135       refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
 136       indpdb=index(controlcard,'PDBSTART')
 137       extconf=(index(controlcard,'EXTCONF').gt.0)
 138       call readi(controlcard,'IPRINT',iprint,0)
 139       call readi(controlcard,'MAXGEN',maxgen,10000)
 140       call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
 141       call readi(controlcard,"KDIAG",kdiag,0)
 142       call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
 143       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
 144      & write (iout,*) "RESCALE_MODE",rescale_mode
 145       split_ene=index(controlcard,'SPLIT_ENE').gt.0
 146       if (index(controlcard,'REGULAR').gt.0.0D0) then
 147         call reada(controlcard,'WEIDIS',weidis,0.1D0)
 148         modecalc=1
 149         refstr=.true.
 150       endif
 151       if (index(controlcard,'CHECKGRAD').gt.0) then
 152         modecalc=5
 153         if (index(controlcard,'CART').gt.0) then
 154           icheckgrad=1
 155         elseif (index(controlcard,'CARINT').gt.0) then
 156           icheckgrad=2
 157         else
 158           icheckgrad=3
 159         endif
 160       elseif (index(controlcard,'THREAD').gt.0) then
 161         modecalc=2
 162         call readi(controlcard,'THREAD',nthread,0)
 163         if (nthread.gt.0) then
 164           call reada(controlcard,'WEIDIS',weidis,0.1D0)
 165         else
 166           if (fg_rank.eq.0)
 167      &    write (iout,'(a)')'A number has to follow the THREAD keyword.'
 168           stop 'Error termination in Read_Control.'
 169         endif
 170       else if (index(controlcard,'MCMA').gt.0) then
 171         modecalc=3
 172       else if (index(controlcard,'MCEE').gt.0) then
 173         modecalc=6
 174       else if (index(controlcard,'MULTCONF').gt.0) then
 175         modecalc=4
 176       else if (index(controlcard,'MAP').gt.0) then
 177         modecalc=7
 178         call readi(controlcard,'MAP',nmap,0)
 179       else if (index(controlcard,'CSA').gt.0) then
 180         modecalc=8
 181 crc      else if (index(controlcard,'ZSCORE').gt.0) then
 182 crc
 183 crc  ZSCORE is rm from UNRES, modecalc=9 is available
 184 crc
 185 crc        modecalc=9
 186 cfcm      else if (index(controlcard,'MCMF').gt.0) then
 187 cfmc        modecalc=10
 188       else if (index(controlcard,'SOFTREG').gt.0) then
 189         modecalc=11
 190       else if (index(controlcard,'CHECK_BOND').gt.0) then
 191         modecalc=-1
 192       else if (index(controlcard,'TEST').gt.0) then
 193         modecalc=-2
 194       else if (index(controlcard,'MD').gt.0) then
 195         modecalc=12
 196       else if (index(controlcard,'RE ').gt.0) then
 197         modecalc=14
 198       endif
 199
 200       lmuca=index(controlcard,'MUCA').gt.0
 201       call readi(controlcard,'MUCADYN',mucadyn,0)
 202       call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
 203       if (lmuca .and. (me.eq.king .or. .not.out1file ))
 204      & then
 205        write (iout,*) 'MUCADYN=',mucadyn
 206        write (iout,*) 'MUCASMOOTH=',muca_smooth
 207       endif
 208
 209       iscode=index(controlcard,'ONE_LETTER')
 210       indphi=index(controlcard,'PHI')
 211       indback=index(controlcard,'BACK')
 212       iranconf=index(controlcard,'RAND_CONF')
 213       i2ndstr=index(controlcard,'USE_SEC_PRED')
 214       gradout=index(controlcard,'GRADOUT').gt.0
 215       gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
 216       call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
 217       if (me.eq.king .or. .not.out1file )
 218      &  write (iout,*) "DISTCHAINMAX",distchainmax
 219
 220       if(me.eq.king.or..not.out1file)
 221      & write (iout,'(2a)') diagmeth(kdiag),
 222      &  ' routine used to diagonalize matrices.'
 223       return
 224       end
 225 c--------------------------------------------------------------------------
 226       subroutine read_REMDpar
 227 C
 228 C Read REMD settings
 229 C
 230       implicit real*8 (a-h,o-z)
 231       include 'DIMENSIONS'
 232       include 'COMMON.IOUNITS'
 233       include 'COMMON.TIME1'
 234       include 'COMMON.MD'
 235 #ifndef LANG0
 236       include 'COMMON.LANGEVIN'
 237 #else
 238       include 'COMMON.LANGEVIN.lang0'
 239 #endif
 240       include 'COMMON.INTERACT'
 241       include 'COMMON.NAMES'
 242       include 'COMMON.GEO'
 243       include 'COMMON.REMD'
 244       include 'COMMON.CONTROL'
 245       include 'COMMON.SETUP'
 246       character*80 ucase
 247       character*320 controlcard
 248       character*3200 controlcard1
 249       integer iremd_m_total
 250
 251       if(me.eq.king.or..not.out1file)
 252      & write (iout,*) "REMD setup"
 253
 254       call card_concat(controlcard)
 255       call readi(controlcard,"NREP",nrep,3)
 256       call readi(controlcard,"NSTEX",nstex,1000)
 257       call reada(controlcard,"RETMIN",retmin,10.0d0)
 258       call reada(controlcard,"RETMAX",retmax,1000.0d0)
 259       mremdsync=(index(controlcard,'SYNC').gt.0)
 260       call readi(controlcard,"NSYN",i_sync_step,100)
 261       restart1file=(index(controlcard,'REST1FILE').gt.0)
 262       traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
 263       call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
 264       if(max_cache_traj_use.gt.max_cache_traj)
 265      &           max_cache_traj_use=max_cache_traj
 266       if(me.eq.king.or..not.out1file) then
 267 cd       if (traj1file) then
 268 crc caching is in testing - NTWX is not ignored
 269 cd        write (iout,*) "NTWX value is ignored"
 270 cd        write (iout,*) "  trajectory is stored to one file by master"
 271 cd        write (iout,*) "  before exchange at NSTEX intervals"
 272 cd       endif
 273        write (iout,*) "NREP= ",nrep
 274        write (iout,*) "NSTEX= ",nstex
 275        write (iout,*) "SYNC= ",mremdsync
 276        write (iout,*) "NSYN= ",i_sync_step
 277        write (iout,*) "TRAJCACHE= ",max_cache_traj_use
 278       endif
 279       remd_tlist=.false.
 280       if (index(controlcard,'TLIST').gt.0) then
 281          remd_tlist=.true.
 282          call card_concat(controlcard1)
 283          read(controlcard1,*) (remd_t(i),i=1,nrep)
 284          if(me.eq.king.or..not.out1file)
 285      &    write (iout,*)'tlist',(remd_t(i),i=1,nrep)
 286       endif
 287       remd_mlist=.false.
 288       if (index(controlcard,'MLIST').gt.0) then
 289          remd_mlist=.true.
 290          call card_concat(controlcard1)
 291          read(controlcard1,*) (remd_m(i),i=1,nrep)
 292          if(me.eq.king.or..not.out1file) then
 293           write (iout,*)'mlist',(remd_m(i),i=1,nrep)
 294           iremd_m_total=0
 295           do i=1,nrep
 296            iremd_m_total=iremd_m_total+remd_m(i)
 297           enddo
 298            write (iout,*) 'Total number of replicas ',iremd_m_total
 299           endif
 300          endif
 301       if(me.eq.king.or..not.out1file)
 302      &   write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
 303       return
 304       end
 305 c--------------------------------------------------------------------------
 306       subroutine read_MDpar
 307 C
 308 C Read MD settings
 309 C
 310       implicit real*8 (a-h,o-z)
 311       include 'DIMENSIONS'
 312       include 'COMMON.IOUNITS'
 313       include 'COMMON.TIME1'
 314       include 'COMMON.MD'
 315 #ifndef LANG0
 316       include 'COMMON.LANGEVIN'
 317 #else
 318       include 'COMMON.LANGEVIN.lang0'
 319 #endif
 320       include 'COMMON.INTERACT'
 321       include 'COMMON.NAMES'
 322       include 'COMMON.GEO'
 323       include 'COMMON.SETUP'
 324       include 'COMMON.CONTROL'
 325       include 'COMMON.SPLITELE'
 326       character*80 ucase
 327       character*320 controlcard
 328
 329       call card_concat(controlcard)
 330       call readi(controlcard,"NSTEP",n_timestep,1000000)
 331       call readi(controlcard,"NTWE",ntwe,100)
 332       call readi(controlcard,"NTWX",ntwx,1000)
 333       call reada(controlcard,"DT",d_time,1.0d-1)
 334       call reada(controlcard,"DVMAX",dvmax,2.0d1)
 335       call reada(controlcard,"DAMAX",damax,1.0d1)
 336       call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
 337       call readi(controlcard,"LANG",lang,0)
 338       RESPA = index(controlcard,"RESPA") .gt. 0
 339       call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
 340       ntime_split0=ntime_split
 341       call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
 342       ntime_split0=ntime_split
 343       call reada(controlcard,"R_CUT",r_cut,2.0d0)
 344       call reada(controlcard,"LAMBDA",rlamb,0.3d0)
 345       rest = index(controlcard,"REST").gt.0
 346       tbf = index(controlcard,"TBF").gt.0
 347       usampl = index(controlcard,"USAMPL").gt.0
 348
 349       mdpdb = index(controlcard,"MDPDB").gt.0
 350       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 351       call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
 352       call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
 353       call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
 354       if (count_reset_moment.eq.0) count_reset_moment=1000000000
 355       call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
 356       reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
 357       reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
 358       if (count_reset_vel.eq.0) count_reset_vel=1000000000
 359       large = index(controlcard,"LARGE").gt.0
 360       print_compon = index(controlcard,"PRINT_COMPON").gt.0
 361       rattle = index(controlcard,"RATTLE").gt.0
 362 c  if performing umbrella sampling, fragments constrained are read from the fragment file
 363       nset=0
 364       if(usampl) then
 365         call read_fragments
 366       endif
 367
 368       if(me.eq.king.or..not.out1file) then
 369        write (iout,*)
 370        write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
 371        write (iout,*)
 372        write (iout,'(a)') "The units are:"
 373        write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
 374        write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",
 375      &  " acceleration: angstrom/(48.9 fs)**2"
 376        write (iout,'(a)') "energy: kcal/mol, temperature: K"
 377        write (iout,*)
 378        write (iout,'(a60,i10)') "Number of time steps:",n_timestep
 379        write (iout,'(a60,f10.5,a)')
 380      &  "Initial time step of numerical integration:",d_time,
 381      &  " natural units"
 382        write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
 383        if (RESPA) then
 384         write (iout,'(2a,i4,a)')
 385      &    "A-MTS algorithm used; initial time step for fast-varying",
 386      &    " short-range forces split into",ntime_split," steps."
 387         write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
 388      &   r_cut," lambda",rlamb
 389        endif
 390        write (iout,'(2a,f10.5)')
 391      &  "Maximum acceleration threshold to reduce the time step",
 392      &  "/increase split number:",damax
 393        write (iout,'(2a,f10.5)')
 394      &  "Maximum predicted energy drift to reduce the timestep",
 395      &  "/increase split number:",edriftmax
 396        write (iout,'(a60,f10.5)')
 397      & "Maximum velocity threshold to reduce velocities:",dvmax
 398        write (iout,'(a60,i10)') "Frequency of property output:",ntwe
 399        write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
 400        if (rattle) write (iout,'(a60)')
 401      &  "Rattle algorithm used to constrain the virtual bonds"
 402       endif
 403       reset_fricmat=1000
 404       if (lang.gt.0) then
 405         call reada(controlcard,"ETAWAT",etawat,0.8904d0)
 406         call reada(controlcard,"RWAT",rwat,1.4d0)
 407         call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
 408         surfarea=index(controlcard,"SURFAREA").gt.0
 409         call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
 410         if(me.eq.king.or..not.out1file)then
 411          write (iout,'(/a,$)') "Langevin dynamics calculation"
 412          if (lang.eq.1) then
 413           write (iout,'(a/)')
 414      &      " with direct integration of Langevin equations"
 415          else if (lang.eq.2) then
 416           write (iout,'(a/)') " with TINKER stochasic MD integrator"
 417          else if (lang.eq.3) then
 418           write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
 419          else if (lang.eq.4) then
 420           write (iout,'(a/)') " in overdamped mode"
 421          else
 422           write (iout,'(//a,i5)')
 423      &      "=========== ERROR: Unknown Langevin dynamics mode:",lang
 424           stop
 425          endif
 426          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 427          write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
 428          write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
 429          write (iout,'(a60,f10.5)')
 430      &   "Scaling factor of the friction forces:",scal_fric
 431          if (surfarea) write (iout,'(2a,i10,a)')
 432      &     "Friction coefficients will be scaled by solvent-accessible",
 433      &     " surface area every",reset_fricmat," steps."
 434         endif
 435 c Calculate friction coefficients and bounds of stochastic forces
 436         eta=6*pi*cPoise*etawat
 437         if(me.eq.king.or..not.out1file)
 438      &   write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:"
 439      &   ,eta
 440         gamp=scal_fric*(pstok+rwat)*eta
 441         stdfp=dsqrt(2*Rb*t_bath/d_time)
 442         do i=1,ntyp
 443           gamsc(i)=scal_fric*(restok(i)+rwat)*eta
 444           stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
 445         enddo
 446         if(me.eq.king.or..not.out1file)then
 447          write (iout,'(/2a/)')
 448      &   "Radii of site types and friction coefficients and std's of",
 449      &   " stochastic forces of fully exposed sites"
 450          write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
 451          do i=1,ntyp
 452           write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),
 453      &     gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
 454          enddo
 455         endif
 456       else if (tbf) then
 457         if(me.eq.king.or..not.out1file)then
 458          write (iout,'(a)') "Berendsen bath calculation"
 459          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 460          write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
 461          if (reset_moment)
 462      &   write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 463      &   count_reset_moment," steps"
 464          if (reset_vel)
 465      &    write (iout,'(a,i10,a)')
 466      &    "Velocities will be reset at random every",count_reset_vel,
 467      &   " steps"
 468         endif
 469       else
 470         if(me.eq.king.or..not.out1file)
 471      &   write (iout,'(a31)') "Microcanonical mode calculation"
 472       endif
 473       if(me.eq.king.or..not.out1file)then
 474        if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
 475        if (usampl) then
 476           write(iout,*) "MD running with constraints."
 477           write(iout,*) "Equilibration time ", eq_time, " mtus."
 478           write(iout,*) "Constraining ", nfrag," fragments."
 479           write(iout,*) "Length of each fragment, weight and q0:"
 480           do iset=1,nset
 481            write (iout,*) "Set of restraints #",iset
 482            do i=1,nfrag
 483               write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),
 484      &           ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
 485            enddo
 486            write(iout,*) "constraints between ", npair, "fragments."
 487            write(iout,*) "constraint pairs, weights and q0:"
 488            do i=1,npair
 489             write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),
 490      &             ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
 491            enddo
 492            write(iout,*) "angle constraints within ", nfrag_back,
 493      &      "backbone fragments."
 494            write(iout,*) "fragment, weights:"
 495            do i=1,nfrag_back
 496             write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),
 497      &         ifrag_back(2,i,iset),wfrag_back(1,i,iset),
 498      &         wfrag_back(2,i,iset),wfrag_back(3,i,iset)
 499            enddo
 500           enddo
 501         iset=mod(kolor,nset)+1
 502        endif
 503       endif
 504       if(me.eq.king.or..not.out1file)
 505      & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
 506       return
 507       end
 508 c------------------------------------------------------------------------------
 509       subroutine molread
 510 C
 511 C Read molecular data.
 512 C
 513       implicit real*8 (a-h,o-z)
 514       include 'DIMENSIONS'
 515 #ifdef MPI
 516       include 'mpif.h'
 517       integer error_msg
 518 #endif
 519       include 'COMMON.IOUNITS'
 520       include 'COMMON.GEO'
 521       include 'COMMON.VAR'
 522       include 'COMMON.INTERACT'
 523       include 'COMMON.LOCAL'
 524       include 'COMMON.NAMES'
 525       include 'COMMON.CHAIN'
 526       include 'COMMON.FFIELD'
 527       include 'COMMON.SBRIDGE'
 528       include 'COMMON.HEADER'
 529       include 'COMMON.CONTROL'
 530       include 'COMMON.DBASE'
 531       include 'COMMON.THREAD'
 532       include 'COMMON.CONTACTS'
 533       include 'COMMON.TORCNSTR'
 534       include 'COMMON.TIME1'
 535       include 'COMMON.BOUNDS'
 536       include 'COMMON.MD'
 537       include 'COMMON.SETUP'
 538       character*4 sequence(maxres)
 539       integer rescode
 540       double precision x(maxvar)
 541       character*256 pdbfile
 542       character*320 weightcard
 543       character*80 weightcard_t,ucase
 544       dimension itype_pdb(maxres)
 545       common /pizda/ itype_pdb
 546       logical seq_comp,fail
 547       double precision energia(0:n_ene)
 548       integer ilen
 549       external ilen
 550 C
 551 C Body
 552 C
 553 C Read weights of the subsequent energy terms.
 554        call card_concat(weightcard)
 555        call reada(weightcard,'WLONG',wlong,1.0D0)
 556        call reada(weightcard,'WSC',wsc,wlong)
 557        call reada(weightcard,'WSCP',wscp,wlong)
 558        call reada(weightcard,'WELEC',welec,1.0D0)
 559        call reada(weightcard,'WVDWPP',wvdwpp,welec)
 560        call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 561        call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 562        call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 563        call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 564        call reada(weightcard,'WTURN3',wturn3,1.0D0)
 565        call reada(weightcard,'WTURN4',wturn4,1.0D0)
 566        call reada(weightcard,'WTURN6',wturn6,1.0D0)
 567        call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 568        call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 569        call reada(weightcard,'WBOND',wbond,1.0D0)
 570        call reada(weightcard,'WTOR',wtor,1.0D0)
 571        call reada(weightcard,'WTORD',wtor_d,1.0D0)
 572        call reada(weightcard,'WANG',wang,1.0D0)
 573        call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 574        call reada(weightcard,'SCAL14',scal14,0.4D0)
 575        call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 576        call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 577        call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 578        call reada(weightcard,'TEMP0',temp0,300.0d0)
 579        if (index(weightcard,'SOFT').gt.0) ipot=6
 580 C 12/1/95 Added weight for the multi-body term WCORR
 581        call reada(weightcard,'WCORRH',wcorr,1.0D0)
 582        if (wcorr4.gt.0.0d0) wcorr=wcorr4
 583        weights(1)=wsc
 584        weights(2)=wscp
 585        weights(3)=welec
 586        weights(4)=wcorr
 587        weights(5)=wcorr5
 588        weights(6)=wcorr6
 589        weights(7)=wel_loc
 590        weights(8)=wturn3
 591        weights(9)=wturn4
 592        weights(10)=wturn6
 593        weights(11)=wang
 594        weights(12)=wscloc
 595        weights(13)=wtor
 596        weights(14)=wtor_d
 597        weights(15)=wstrain
 598        weights(16)=wvdwpp
 599        weights(17)=wbond
 600        weights(18)=scal14
 601        weights(21)=wsccor
 602       if(me.eq.king.or..not.out1file)
 603      & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 604      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 605      &  wturn4,wturn6
 606    10 format (/'Energy-term weights (unscaled):'//
 607      & 'WSCC=   ',f10.6,' (SC-SC)'/
 608      & 'WSCP=   ',f10.6,' (SC-p)'/
 609      & 'WELEC=  ',f10.6,' (p-p electr)'/
 610      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 611      & 'WBOND=  ',f10.6,' (stretching)'/
 612      & 'WANG=   ',f10.6,' (bending)'/
 613      & 'WSCLOC= ',f10.6,' (SC local)'/
 614      & 'WTOR=   ',f10.6,' (torsional)'/
 615      & 'WTORD=  ',f10.6,' (double torsional)'/
 616      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 617      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 618      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 619      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 620      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 621      & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
 622      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 623      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 624      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 625       if(me.eq.king.or..not.out1file)then
 626        if (wcorr4.gt.0.0d0) then
 627         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
 628      &   'between contact pairs of peptide groups'
 629         write (iout,'(2(a,f5.3/))')
 630      &  'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
 631      &  'Range of quenching the correlation terms:',2*delt_corr
 632        else if (wcorr.gt.0.0d0) then
 633         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
 634      &   'between contact pairs of peptide groups'
 635        endif
 636        write (iout,'(a,f8.3)')
 637      &  'Scaling factor of 1,4 SC-p interactions:',scal14
 638        write (iout,'(a,f8.3)')
 639      &  'General scaling factor of SC-p interactions:',scalscp
 640       endif
 641       r0_corr=cutoff_corr-delt_corr
 642       do i=1,20
 643         aad(i,1)=scalscp*aad(i,1)
 644         aad(i,2)=scalscp*aad(i,2)
 645         bad(i,1)=scalscp*bad(i,1)
 646         bad(i,2)=scalscp*bad(i,2)
 647       enddo
 648       call rescale_weights(t_bath)
 649       if(me.eq.king.or..not.out1file)
 650      & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 651      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 652      &  wturn4,wturn6
 653    22 format (/'Energy-term weights (scaled):'//
 654      & 'WSCC=   ',f10.6,' (SC-SC)'/
 655      & 'WSCP=   ',f10.6,' (SC-p)'/
 656      & 'WELEC=  ',f10.6,' (p-p electr)'/
 657      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 658      & 'WBOND=  ',f10.6,' (stretching)'/
 659      & 'WANG=   ',f10.6,' (bending)'/
 660      & 'WSCLOC= ',f10.6,' (SC local)'/
 661      & 'WTOR=   ',f10.6,' (torsional)'/
 662      & 'WTORD=  ',f10.6,' (double torsional)'/
 663      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 664      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 665      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 666      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 667      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 668      & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
 669      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 670      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 671      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 672       if(me.eq.king.or..not.out1file)
 673      & write (iout,*) "Reference temperature for weights calculation:",
 674      &  temp0
 675       call reada(weightcard,"D0CM",d0cm,3.78d0)
 676       call reada(weightcard,"AKCM",akcm,15.1d0)
 677       call reada(weightcard,"AKTH",akth,11.0d0)
 678       call reada(weightcard,"AKCT",akct,12.0d0)
 679       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 680       call reada(weightcard,"V2SS",v2ss,7.61d0)
 681       call reada(weightcard,"V3SS",v3ss,13.7d0)
 682       call reada(weightcard,"EBR",ebr,-5.50D0)
 683       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 684       do i=1,maxres
 685         dyn_ss_mask(i)=.false.
 686       enddo
 687       do i=1,maxres-1
 688         do j=i+1,maxres
 689           dyn_ssbond_ij(i,j)=1.0d300
 690         enddo
 691       enddo
 692       call reada(weightcard,"HT",Ht,0.0D0)
 693       if (dyn_ss) then
 694         ss_depth=ebr/wsc-0.25*eps(1,1)
 695         Ht=Ht/wsc-0.25*eps(1,1)
 696         akcm=akcm*wstrain/wsc
 697         akth=akth*wstrain/wsc
 698         akct=akct*wstrain/wsc
 699         v1ss=v1ss*wstrain/wsc
 700         v2ss=v2ss*wstrain/wsc
 701         v3ss=v3ss*wstrain/wsc
 702       else
 703         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 704       endif
 705
 706       if(me.eq.king.or..not.out1file) then
 707        write (iout,*) "Parameters of the SS-bond potential:"
 708        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
 709      & " AKCT",akct
 710        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 711        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 712        write (iout,*)" HT",Ht
 713        print *,'indpdb=',indpdb,' pdbref=',pdbref
 714       endif
 715       if (indpdb.gt.0 .or. pdbref) then
 716         read(inp,'(a)') pdbfile
 717         if(me.eq.king.or..not.out1file)
 718      &   write (iout,'(2a)') 'PDB data will be read from file ',
 719      &   pdbfile(:ilen(pdbfile))
 720         open(ipdbin,file=pdbfile,status='old',err=33)
 721         goto 34
 722   33    write (iout,'(a)') 'Error opening PDB file.'
 723         stop
 724   34    continue
 725 c        print *,'Begin reading pdb data'
 726         call readpdb
 727 c        print *,'Finished reading pdb data'
 728         if(me.eq.king.or..not.out1file)
 729      &   write (iout,'(a,i3,a,i3)')'nsup=',nsup,
 730      &   ' nstart_sup=',nstart_sup
 731         do i=1,nres
 732           itype_pdb(i)=itype(i)
 733         enddo
 734         close (ipdbin)
 735         nnt=nstart_sup
 736         nct=nstart_sup+nsup-1
 737         call contact(.false.,ncont_ref,icont_ref,co)
 738
 739         if (sideadd) then
 740          if(me.eq.king.or..not.out1file)
 741      &    write(iout,*)'Adding sidechains'
 742          maxsi=1000
 743          do i=2,nres-1
 744           iti=itype(i)
 745           if (iti.ne.10 .and. itype(i).ne.21) then
 746             nsi=0
 747             fail=.true.
 748             do while (fail.and.nsi.le.maxsi)
 749               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 750               nsi=nsi+1
 751             enddo
 752             if(fail) write(iout,*)'Adding sidechain failed for res ',
 753      &              i,' after ',nsi,' trials'
 754           endif
 755          enddo
 756         endif
 757       endif
 758       if (indpdb.eq.0) then
 759 C Read sequence if not taken from the pdb file.
 760         read (inp,*) nres
 761 c        print *,'nres=',nres
 762         if (iscode.gt.0) then
 763           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 764         else
 765           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 766         endif
 767 C Convert sequence to numeric code
 768         do i=1,nres
 769           itype(i)=rescode(i,sequence(i),iscode)
 770         enddo
 771 C Assign initial virtual bond lengths
 772         do i=2,nres
 773           vbld(i)=vbl
 774           vbld_inv(i)=vblinv
 775         enddo
 776         do i=2,nres-1
 777           vbld(i+nres)=dsc(itype(i))
 778           vbld_inv(i+nres)=dsc_inv(itype(i))
 779 c          write (iout,*) "i",i," itype",itype(i),
 780 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 781         enddo
 782       endif
 783 c      print *,nres
 784 c      print '(20i4)',(itype(i),i=1,nres)
 785       do i=1,nres
 786 #ifdef PROCOR
 787         if (itype(i).eq.21 .or. itype(i+1).eq.21) then
 788 #else
 789         if (itype(i).eq.21) then
 790 #endif
 791           itel(i)=0
 792 #ifdef PROCOR
 793         else if (itype(i+1).ne.20) then
 794 #else
 795         else if (itype(i).ne.20) then
 796 #endif
 797           itel(i)=1
 798         else
 799           itel(i)=2
 800         endif
 801       enddo
 802       if(me.eq.king.or..not.out1file)then
 803        write (iout,*) "ITEL"
 804        do i=1,nres-1
 805          write (iout,*) i,itype(i),itel(i)
 806        enddo
 807        print *,'Call Read_Bridge.'
 808       endif
 809       call read_bridge
 810 C 8/13/98 Set limits to generating the dihedral angles
 811       do i=1,nres
 812         phibound(1,i)=-pi
 813         phibound(2,i)=pi
 814       enddo
 815       read (inp,*) ndih_constr
 816       if (ndih_constr.gt.0) then
 817         read (inp,*) ftors
 818         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
 819         if(me.eq.king.or..not.out1file)then
 820          write (iout,*)
 821      &   'There are',ndih_constr,' constraints on phi angles.'
 822          do i=1,ndih_constr
 823           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
 824          enddo
 825         endif
 826         do i=1,ndih_constr
 827           phi0(i)=deg2rad*phi0(i)
 828           drange(i)=deg2rad*drange(i)
 829         enddo
 830         if(me.eq.king.or..not.out1file)
 831      &   write (iout,*) 'FTORS',ftors
 832         do i=1,ndih_constr
 833           ii = idih_constr(i)
 834           phibound(1,ii) = phi0(i)-drange(i)
 835           phibound(2,ii) = phi0(i)+drange(i)
 836         enddo
 837       endif
 838       nnt=1
 839 #ifdef MPI
 840       if (me.eq.king) then
 841 #endif
 842        write (iout,'(a)') 'Boundaries in phi angle sampling:'
 843        do i=1,nres
 844          write (iout,'(a3,i5,2f10.1)')
 845      &   restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
 846        enddo
 847 #ifdef MP
 848       endif
 849 #endif
 850       nct=nres
 851 cd      print *,'NNT=',NNT,' NCT=',NCT
 852       if (itype(1).eq.21) nnt=2
 853       if (itype(nres).eq.21) nct=nct-1
 854       if (pdbref) then
 855         if(me.eq.king.or..not.out1file)
 856      &   write (iout,'(a,i3)') 'nsup=',nsup
 857         nstart_seq=nnt
 858         if (nsup.le.(nct-nnt+1)) then
 859           do i=0,nct-nnt+1-nsup
 860             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
 861               nstart_seq=nnt+i
 862               goto 111
 863             endif
 864           enddo
 865           write (iout,'(a)')
 866      &            'Error - sequences to be superposed do not match.'
 867           stop
 868         else
 869           do i=0,nsup-(nct-nnt+1)
 870             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
 871      &      then
 872               nstart_sup=nstart_sup+i
 873               nsup=nct-nnt+1
 874               goto 111
 875             endif
 876           enddo
 877           write (iout,'(a)')
 878      &            'Error - sequences to be superposed do not match.'
 879         endif
 880   111   continue
 881         if (nsup.eq.0) nsup=nct-nnt
 882         if (nstart_sup.eq.0) nstart_sup=nnt
 883         if (nstart_seq.eq.0) nstart_seq=nnt
 884         if(me.eq.king.or..not.out1file)
 885      &   write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
 886      &                 ' nstart_seq=',nstart_seq
 887       endif
 888 c--- Zscore rms -------
 889       if (nz_start.eq.0) nz_start=nnt
 890       if (nz_end.eq.0 .and. nsup.gt.0) then
 891         nz_end=nnt+nsup-1
 892       else if (nz_end.eq.0) then
 893         nz_end=nct
 894       endif
 895       if(me.eq.king.or..not.out1file)then
 896        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
 897        write (iout,*) 'IZ_SC=',iz_sc
 898       endif
 899 c----------------------
 900       call init_int_table
 901       if (refstr) then
 902         if (.not.pdbref) then
 903           call read_angles(inp,*38)
 904           goto 39
 905    38     write (iout,'(a)') 'Error reading reference structure.'
 906 #ifdef MPI
 907           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
 908           stop 'Error reading reference structure'
 909 #endif
 910    39     call chainbuild
 911           call setup_var
 912 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
 913           nstart_sup=nnt
 914           nstart_seq=nnt
 915           nsup=nct-nnt+1
 916           kkk=1
 917           do i=1,2*nres
 918             do j=1,3
 919               cref(j,i,kkk)=c(j,i)
 920             enddo
 921           enddo
 922           call contact(.true.,ncont_ref,icont_ref,co)
 923         endif
 924 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
 925         call flush(iout)
 926         if (constr_dist.gt.0) call read_dist_constr
 927         write (iout,*) "After read_dist_constr nhpb",nhpb
 928         call hpb_partition
 929         if(me.eq.king.or..not.out1file)
 930      &   write (iout,*) 'Contact order:',co
 931         if (pdbref) then
 932         if(me.eq.king.or..not.out1file)
 933      &   write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
 934         do i=1,ncont_ref
 935           do j=1,2
 936             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
 937           enddo
 938           if(me.eq.king.or..not.out1file)
 939      &     write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',
 940      &     icont_ref(1,i),' ',
 941      &     restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
 942         enddo
 943         endif
 944       endif
 945       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
 946      &    .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
 947      &    modecalc.ne.10) then
 948 C If input structure hasn't been supplied from the PDB file read or generate
 949 C initial geometry.
 950         if (iranconf.eq.0 .and. .not. extconf) then
 951           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
 952      &     write (iout,'(a)') 'Initial geometry will be read in.'
 953           if (read_cart) then
 954             read(inp,'(8f10.5)',end=36,err=36)
 955      &       ((c(l,k),l=1,3),k=1,nres),
 956      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
 957             write (iout,*) "Exit READ_CART"
 958             write (iout,'(8f10.5)')
 959      &       ((c(l,k),l=1,3),k=1,nres),
 960      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
 961             call int_from_cart1(.true.)
 962             write (iout,*) "Finish INT_TO_CART"
 963             do i=1,nres-1
 964               do j=1,3
 965                 dc(j,i)=c(j,i+1)-c(j,i)
 966                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
 967               enddo
 968             enddo
 969             do i=nnt,nct
 970               if (itype(i).ne.10 .and. itype(i).ne.21) then
 971                 do j=1,3
 972                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
 973                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
 974                 enddo
 975               endif
 976             enddo
 977             return
 978           else
 979             call read_angles(inp,*36)
 980           endif
 981           goto 37
 982    36     write (iout,'(a)') 'Error reading angle file.'
 983 #ifdef MPI
 984           call mpi_finalize( MPI_COMM_WORLD,IERR )
 985 #endif
 986           stop 'Error reading angle file.'
 987    37     continue
 988         else if (extconf) then
 989          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0)
 990      &    write (iout,'(a)') 'Extended chain initial geometry.'
 991          do i=3,nres
 992           theta(i)=90d0*deg2rad
 993          enddo
 994          do i=4,nres
 995           phi(i)=180d0*deg2rad
 996          enddo
 997          do i=2,nres-1
 998           alph(i)=110d0*deg2rad
 999          enddo
1000          do i=2,nres-1
1001           omeg(i)=-120d0*deg2rad
1002          enddo
1003         else
1004           if(me.eq.king.or..not.out1file)
1005      &     write (iout,'(a)') 'Random-generated initial geometry.'
1006
1007
1008 #ifdef MPI
1009           if (me.eq.king  .or. fg_rank.eq.0 .and. (
1010      &           modecalc.eq.12 .or. modecalc.eq.14) ) then
1011 #endif
1012             do itrial=1,100
1013               itmp=1
1014               call gen_rand_conf(itmp,*30)
1015               goto 40
1016    30         write (iout,*) 'Failed to generate random conformation',
1017      &          ', itrial=',itrial
1018               write (*,*) 'Processor:',me,
1019      &          ' Failed to generate random conformation',
1020      &          ' itrial=',itrial
1021               call intout
1022
1023 #ifdef AIX
1024               call flush_(iout)
1025 #else
1026               call flush(iout)
1027 #endif
1028             enddo
1029             write (iout,'(a,i3,a)') 'Processor:',me,
1030      &        ' error in generating random conformation.'
1031             write (*,'(a,i3,a)') 'Processor:',me,
1032      &        ' error in generating random conformation.'
1033             call flush(iout)
1034 #ifdef MPI
1035             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1036    40       continue
1037           endif
1038 #else
1039           do itrial=1,100
1040             itmp=1
1041             call gen_rand_conf(itmp,*30)
1042             goto 40
1043    30       write (iout,*) 'Failed to generate random conformation',
1044      &        ', itrial=',itrial
1045             write (*,*) 'Failed to generate random conformation',
1046      &        ', itrial=',itrial
1047           enddo
1048           write (iout,'(a,i3,a)') 'Processor:',me,
1049      &      ' error in generating random conformation.'
1050           write (*,'(a,i3,a)') 'Processor:',me,
1051      &      ' error in generating random conformation.'
1052           stop
1053    40     continue
1054 #endif
1055         endif
1056       elseif (modecalc.eq.4) then
1057         read (inp,'(a)') intinname
1058         open (intin,file=intinname,status='old',err=333)
1059         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0)
1060      &  write (iout,'(a)') 'intinname',intinname
1061         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1062         goto 334
1063   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1064 #ifdef MPI
1065         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1066 #endif
1067         stop 'Error opening angle file.'
1068   334   continue
1069
1070       endif
1071 C Generate distance constraints, if the PDB structure is to be regularized.
1072       if (nthread.gt.0) then
1073         call read_threadbase
1074       endif
1075       call setup_var
1076       if (me.eq.king .or. .not. out1file)
1077      & call intout
1078       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1079         write (iout,'(/a,i3,a)')
1080      &  'The chain contains',ns,' disulfide-bridging cysteines.'
1081         write (iout,'(20i4)') (iss(i),i=1,ns)
1082        if (dyn_ss) then
1083           write(iout,*)"Running with dynamic disulfide-bond formation"
1084        else
1085         write (iout,'(/a/)') 'Pre-formed links are:'
1086         do i=1,nss
1087           i1=ihpb(i)-nres
1088           i2=jhpb(i)-nres
1089           it1=itype(i1)
1090           it2=itype(i2)
1091           write (iout,'(2a,i3,3a,i3,a,3f10.3)')
1092      &    restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
1093      &    ebr,forcon(i)
1094         enddo
1095         write (iout,'(a)')
1096        endif
1097       endif
1098       if (ns.gt.0.and.dyn_ss) then
1099           do i=nss+1,nhpb
1100             ihpb(i-nss)=ihpb(i)
1101             jhpb(i-nss)=jhpb(i)
1102             forcon(i-nss)=forcon(i)
1103             dhpb(i-nss)=dhpb(i)
1104           enddo
1105           nhpb=nhpb-nss
1106           nss=0
1107           call hpb_partition
1108           do i=1,ns
1109             dyn_ss_mask(iss(i))=.true.
1110           enddo
1111       endif
1112       if (i2ndstr.gt.0) call secstrp2dihc
1113 c      call geom_to_var(nvar,x)
1114 c      call etotal(energia(0))
1115 c      call enerprint(energia(0))
1116 c      call briefout(0,etot)
1117 c      stop
1118 cd    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1119 cd    write (iout,'(a)') 'Variable list:'
1120 cd    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1121 #ifdef MPI
1122       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file))
1123      &  write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
1124      &  'Processor',myrank,': end reading molecular data.'
1125 #endif
1126       return
1127       end
1128 c--------------------------------------------------------------------------
1129       logical function seq_comp(itypea,itypeb,length)
1130       implicit none
1131       integer length,itypea(length),itypeb(length)
1132       integer i
1133       do i=1,length
1134         if (itypea(i).ne.itypeb(i)) then
1135           seq_comp=.false.
1136           return
1137         endif
1138       enddo
1139       seq_comp=.true.
1140       return
1141       end
1142 c-----------------------------------------------------------------------------
1143       subroutine read_bridge
1144 C Read information about disulfide bridges.
1145       implicit real*8 (a-h,o-z)
1146       include 'DIMENSIONS'
1147 #ifdef MPI
1148       include 'mpif.h'
1149 #endif
1150       include 'COMMON.IOUNITS'
1151       include 'COMMON.GEO'
1152       include 'COMMON.VAR'
1153       include 'COMMON.INTERACT'
1154       include 'COMMON.LOCAL'
1155       include 'COMMON.NAMES'
1156       include 'COMMON.CHAIN'
1157       include 'COMMON.FFIELD'
1158       include 'COMMON.SBRIDGE'
1159       include 'COMMON.HEADER'
1160       include 'COMMON.CONTROL'
1161       include 'COMMON.DBASE'
1162       include 'COMMON.THREAD'
1163       include 'COMMON.TIME1'
1164       include 'COMMON.SETUP'
1165 C Read bridging residues.
1166       read (inp,*) ns,(iss(i),i=1,ns)
1167       print *,'ns=',ns
1168       if(me.eq.king.or..not.out1file)
1169      &  write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
1170 C Check whether the specified bridging residues are cystines.
1171       do i=1,ns
1172         if (itype(iss(i)).ne.1) then
1173           if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
1174      &   'Do you REALLY think that the residue ',
1175      &    restyp(itype(iss(i))),i,
1176      &   ' can form a disulfide bridge?!!!'
1177           write (*,'(2a,i3,a)')
1178      &   'Do you REALLY think that the residue ',
1179      &    restyp(itype(iss(i))),i,
1180      &   ' can form a disulfide bridge?!!!'
1181 #ifdef MPI
1182          call MPI_Finalize(MPI_COMM_WORLD,ierror)
1183          stop
1184 #endif
1185         endif
1186       enddo
1187 C Read preformed bridges.
1188       if (ns.gt.0) then
1189       read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
1190       if(fg_rank.eq.0)
1191      & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
1192       if (nss.gt.0) then
1193         nhpb=nss
1194 C Check if the residues involved in bridges are in the specified list of
1195 C bridging residues.
1196         do i=1,nss
1197           do j=1,i-1
1198             if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
1199      &      .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
1200               write (iout,'(a,i3,a)') 'Disulfide pair',i,
1201      &      ' contains residues present in other pairs.'
1202               write (*,'(a,i3,a)') 'Disulfide pair',i,
1203      &      ' contains residues present in other pairs.'
1204 #ifdef MPI
1205               call MPI_Finalize(MPI_COMM_WORLD,ierror)
1206               stop
1207 #endif
1208             endif
1209           enddo
1210           do j=1,ns
1211             if (ihpb(i).eq.iss(j)) goto 10
1212           enddo
1213           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1214    10     continue
1215           do j=1,ns
1216             if (jhpb(i).eq.iss(j)) goto 20
1217           enddo
1218           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1219    20     continue
1220           dhpb(i)=dbr
1221           forcon(i)=fbr
1222         enddo
1223         do i=1,nss
1224           ihpb(i)=ihpb(i)+nres
1225           jhpb(i)=jhpb(i)+nres
1226         enddo
1227       endif
1228       endif
1229       return
1230       end
1231 c----------------------------------------------------------------------------
1232       subroutine read_x(kanal,*)
1233       implicit real*8 (a-h,o-z)
1234       include 'DIMENSIONS'
1235       include 'COMMON.GEO'
1236       include 'COMMON.VAR'
1237       include 'COMMON.CHAIN'
1238       include 'COMMON.IOUNITS'
1239       include 'COMMON.CONTROL'
1240       include 'COMMON.LOCAL'
1241       include 'COMMON.INTERACT'
1242 c Read coordinates from input
1243 c
1244       read(kanal,'(8f10.5)',end=10,err=10)
1245      &  ((c(l,k),l=1,3),k=1,nres),
1246      &  ((c(l,k+nres),l=1,3),k=nnt,nct)
1247       do j=1,3
1248         c(j,nres+1)=c(j,1)
1249         c(j,2*nres)=c(j,nres)
1250       enddo
1251       call int_from_cart1(.false.)
1252       do i=1,nres-1
1253         do j=1,3
1254           dc(j,i)=c(j,i+1)-c(j,i)
1255           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
1256         enddo
1257       enddo
1258       do i=nnt,nct
1259         if (itype(i).ne.10 .and. itype(i).ne.21) then
1260           do j=1,3
1261             dc(j,i+nres)=c(j,i+nres)-c(j,i)
1262             dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
1263           enddo
1264         endif
1265       enddo
1266
1267       return
1268    10 return1
1269       end
1270 c----------------------------------------------------------------------------
1271       subroutine read_threadbase
1272       implicit real*8 (a-h,o-z)
1273       include 'DIMENSIONS'
1274       include 'COMMON.IOUNITS'
1275       include 'COMMON.GEO'
1276       include 'COMMON.VAR'
1277       include 'COMMON.INTERACT'
1278       include 'COMMON.LOCAL'
1279       include 'COMMON.NAMES'
1280       include 'COMMON.CHAIN'
1281       include 'COMMON.FFIELD'
1282       include 'COMMON.SBRIDGE'
1283       include 'COMMON.HEADER'
1284       include 'COMMON.CONTROL'
1285       include 'COMMON.DBASE'
1286       include 'COMMON.THREAD'
1287       include 'COMMON.TIME1'
1288 C Read pattern database for threading.
1289       read (icbase,*) nseq
1290       do i=1,nseq
1291         read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1292      &   nres_base(2,i),nres_base(3,i)
1293         read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1294      &   nres_base(1,i))
1295 c       write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1296 c    &   nres_base(2,i),nres_base(3,i)
1297 c       write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1298 c    &   nres_base(1,i))
1299       enddo
1300       close (icbase)
1301       if (weidis.eq.0.0D0) weidis=0.1D0
1302       do i=nnt,nct
1303         do j=i+2,nct
1304           nhpb=nhpb+1
1305           ihpb(nhpb)=i
1306           jhpb(nhpb)=j
1307           forcon(nhpb)=weidis
1308         enddo
1309       enddo
1310       read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl)
1311       write (iout,'(a,i5)') 'nexcl: ',nexcl
1312       write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl)
1313       return
1314       end
1315 c------------------------------------------------------------------------------
1316       subroutine setup_var
1317       implicit real*8 (a-h,o-z)
1318       include 'DIMENSIONS'
1319       include 'COMMON.IOUNITS'
1320       include 'COMMON.GEO'
1321       include 'COMMON.VAR'
1322       include 'COMMON.INTERACT'
1323       include 'COMMON.LOCAL'
1324       include 'COMMON.NAMES'
1325       include 'COMMON.CHAIN'
1326       include 'COMMON.FFIELD'
1327       include 'COMMON.SBRIDGE'
1328       include 'COMMON.HEADER'
1329       include 'COMMON.CONTROL'
1330       include 'COMMON.DBASE'
1331       include 'COMMON.THREAD'
1332       include 'COMMON.TIME1'
1333 C Set up variable list.
1334       ntheta=nres-2
1335       nphi=nres-3
1336       nvar=ntheta+nphi
1337       nside=0
1338       do i=2,nres-1
1339         if (itype(i).ne.10 .and. itype(i).ne.21) then
1340           nside=nside+1
1341           ialph(i,1)=nvar+nside
1342           ialph(nside,2)=i
1343         endif
1344       enddo
1345       if (indphi.gt.0) then
1346         nvar=nphi
1347       else if (indback.gt.0) then
1348         nvar=nphi+ntheta
1349       else
1350         nvar=nvar+2*nside
1351       endif
1352 cd    write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
1353       return
1354       end
1355 c----------------------------------------------------------------------------
1356       subroutine gen_dist_constr
1357 C Generate CA distance constraints.
1358       implicit real*8 (a-h,o-z)
1359       include 'DIMENSIONS'
1360       include 'COMMON.IOUNITS'
1361       include 'COMMON.GEO'
1362       include 'COMMON.VAR'
1363       include 'COMMON.INTERACT'
1364       include 'COMMON.LOCAL'
1365       include 'COMMON.NAMES'
1366       include 'COMMON.CHAIN'
1367       include 'COMMON.FFIELD'
1368       include 'COMMON.SBRIDGE'
1369       include 'COMMON.HEADER'
1370       include 'COMMON.CONTROL'
1371       include 'COMMON.DBASE'
1372       include 'COMMON.THREAD'
1373       include 'COMMON.TIME1'
1374       dimension itype_pdb(maxres)
1375       common /pizda/ itype_pdb
1376       character*2 iden
1377 cd      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
1378 cd      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
1379 cd     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
1380 cd     & ' nsup',nsup
1381       do i=nstart_sup,nstart_sup+nsup-1
1382 cd      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
1383 cd     &    ' seq_pdb', restyp(itype_pdb(i))
1384         do j=i+2,nstart_sup+nsup-1
1385           nhpb=nhpb+1
1386           ihpb(nhpb)=i+nstart_seq-nstart_sup
1387           jhpb(nhpb)=j+nstart_seq-nstart_sup
1388           forcon(nhpb)=weidis
1389           dhpb(nhpb)=dist(i,j)
1390         enddo
1391       enddo
1392 cd      write (iout,'(a)') 'Distance constraints:'
1393 cd      do i=nss+1,nhpb
1394 cd        ii=ihpb(i)
1395 cd        jj=jhpb(i)
1396 cd        iden='CA'
1397 cd        if (ii.gt.nres) then
1398 cd          iden='SC'
1399 cd          ii=ii-nres
1400 cd          jj=jj-nres
1401 cd        endif
1402 cd        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
1403 cd     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
1404 cd     &  dhpb(i),forcon(i)
1405 cd      enddo
1406       return
1407       end
1408 c----------------------------------------------------------------------------
1409       subroutine map_read
1410       implicit real*8 (a-h,o-z)
1411       include 'DIMENSIONS'
1412       include 'COMMON.MAP'
1413       include 'COMMON.IOUNITS'
1414       character*3 angid(4) /'THE','PHI','ALP','OME'/
1415       character*80 mapcard,ucase
1416       do imap=1,nmap
1417         read (inp,'(a)') mapcard
1418         mapcard=ucase(mapcard)
1419         if (index(mapcard,'PHI').gt.0) then
1420           kang(imap)=1
1421         else if (index(mapcard,'THE').gt.0) then
1422           kang(imap)=2
1423         else if (index(mapcard,'ALP').gt.0) then
1424           kang(imap)=3
1425         else if (index(mapcard,'OME').gt.0) then
1426           kang(imap)=4
1427         else
1428           write(iout,'(a)')'Error - illegal variable spec in MAP card.'
1429           stop 'Error - illegal variable spec in MAP card.'
1430         endif
1431         call readi (mapcard,'RES1',res1(imap),0)
1432         call readi (mapcard,'RES2',res2(imap),0)
1433         if (res1(imap).eq.0) then
1434           res1(imap)=res2(imap)
1435         else if (res2(imap).eq.0) then
1436           res2(imap)=res1(imap)
1437         endif
1438         if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
1439           write (iout,'(a)')
1440      &    'Error - illegal definition of variable group in MAP.'
1441           stop 'Error - illegal definition of variable group in MAP.'
1442         endif
1443         call reada(mapcard,'FROM',ang_from(imap),0.0D0)
1444         call reada(mapcard,'TO',ang_to(imap),0.0D0)
1445         call readi(mapcard,'NSTEP',nstep(imap),0)
1446         if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
1447           write (iout,'(a)')
1448      &     'Illegal boundary and/or step size specification in MAP.'
1449           stop 'Illegal boundary and/or step size specification in MAP.'
1450         endif
1451       enddo ! imap
1452       return
1453       end
1454 c----------------------------------------------------------------------------
1455       subroutine csaread
1456       implicit real*8 (a-h,o-z)
1457       include 'DIMENSIONS'
1458       include 'COMMON.IOUNITS'
1459       include 'COMMON.GEO'
1460       include 'COMMON.CSA'
1461       include 'COMMON.BANK'
1462       include 'COMMON.CONTROL'
1463       character*80 ucase
1464       character*620 mcmcard
1465       call card_concat(mcmcard)
1466
1467       call readi(mcmcard,'NCONF',nconf,50)
1468       call readi(mcmcard,'NADD',nadd,0)
1469       call readi(mcmcard,'JSTART',jstart,1)
1470       call readi(mcmcard,'JEND',jend,1)
1471       call readi(mcmcard,'NSTMAX',nstmax,500000)
1472       call readi(mcmcard,'N0',n0,1)
1473       call readi(mcmcard,'N1',n1,6)
1474       call readi(mcmcard,'N2',n2,4)
1475       call readi(mcmcard,'N3',n3,0)
1476       call readi(mcmcard,'N4',n4,0)
1477       call readi(mcmcard,'N5',n5,0)
1478       call readi(mcmcard,'N6',n6,10)
1479       call readi(mcmcard,'N7',n7,0)
1480       call readi(mcmcard,'N8',n8,0)
1481       call readi(mcmcard,'N9',n9,0)
1482       call readi(mcmcard,'N14',n14,0)
1483       call readi(mcmcard,'N15',n15,0)
1484       call readi(mcmcard,'N16',n16,0)
1485       call readi(mcmcard,'N17',n17,0)
1486       call readi(mcmcard,'N18',n18,0)
1487
1488       vdisulf=(index(mcmcard,'DYNSS').gt.0)
1489
1490       call readi(mcmcard,'NDIFF',ndiff,2)
1491       call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
1492       call readi(mcmcard,'IS1',is1,1)
1493       call readi(mcmcard,'IS2',is2,8)
1494       call readi(mcmcard,'NRAN0',nran0,4)
1495       call readi(mcmcard,'NRAN1',nran1,2)
1496       call readi(mcmcard,'IRR',irr,1)
1497       call readi(mcmcard,'NSEED',nseed,20)
1498       call readi(mcmcard,'NTOTAL',ntotal,10000)
1499       call reada(mcmcard,'CUT1',cut1,2.0d0)
1500       call reada(mcmcard,'CUT2',cut2,5.0d0)
1501       call reada(mcmcard,'ESTOP',estop,-3000.0d0)
1502       call readi(mcmcard,'ICMAX',icmax,3)
1503       call readi(mcmcard,'IRESTART',irestart,0)
1504 c!bankt      call readi(mcmcard,'NBANKTM',ntbankm,0)
1505       ntbankm=0
1506 c!bankt
1507       call reada(mcmcard,'DELE',dele,20.0d0)
1508       call reada(mcmcard,'DIFCUT',difcut,720.0d0)
1509       call readi(mcmcard,'IREF',iref,0)
1510       call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
1511       call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
1512       call readi(mcmcard,'NCONF_IN',nconf_in,0)
1513       call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
1514       write (iout,*) "NCONF_IN",nconf_in
1515       return
1516       end
1517 c----------------------------------------------------------------------------
1518 cfmc      subroutine mcmfread
1519 cfmc      implicit real*8 (a-h,o-z)
1520 cfmc      include 'DIMENSIONS'
1521 cfmc      include 'COMMON.MCMF'
1522 cfmc      include 'COMMON.IOUNITS'
1523 cfmc      include 'COMMON.GEO'
1524 cfmc      character*80 ucase
1525 cfmc      character*620 mcmcard
1526 cfmc      call card_concat(mcmcard)
1527 cfmc
1528 cfmc      call readi(mcmcard,'MAXRANT',maxrant,1000)
1529 cfmc      write(iout,*)'MAXRANT=',maxrant
1530 cfmc      call readi(mcmcard,'MAXFAM',maxfam,maxfam_p)
1531 cfmc      write(iout,*)'MAXFAM=',maxfam
1532 cfmc      call readi(mcmcard,'NNET1',nnet1,5)
1533 cfmc      write(iout,*)'NNET1=',nnet1
1534 cfmc      call readi(mcmcard,'NNET2',nnet2,4)
1535 cfmc      write(iout,*)'NNET2=',nnet2
1536 cfmc      call readi(mcmcard,'NNET3',nnet3,4)
1537 cfmc      write(iout,*)'NNET3=',nnet3
1538 cfmc      call readi(mcmcard,'ILASTT',ilastt,0)
1539 cfmc      write(iout,*)'ILASTT=',ilastt
1540 cfmc      call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf)
1541 cfmc      write(iout,*)'MAXSTR=',maxstr
1542 cfmc      maxstr_f=maxstr/maxfam
1543 cfmc      write(iout,*)'MAXSTR_F=',maxstr_f
1544 cfmc      call readi(mcmcard,'NMCMF',nmcmf,10)
1545 cfmc      write(iout,*)'NMCMF=',nmcmf
1546 cfmc      call readi(mcmcard,'IFOCUS',ifocus,nmcmf)
1547 cfmc      write(iout,*)'IFOCUS=',ifocus
1548 cfmc      call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000)
1549 cfmc      write(iout,*)'NLOCMCMF=',nlocmcmf
1550 cfmc      call readi(mcmcard,'INTPRT',intprt,1000)
1551 cfmc      write(iout,*)'INTPRT=',intprt
1552 cfmc      call readi(mcmcard,'IPRT',iprt,100)
1553 cfmc      write(iout,*)'IPRT=',iprt
1554 cfmc      call readi(mcmcard,'IMAXTR',imaxtr,100)
1555 cfmc      write(iout,*)'IMAXTR=',imaxtr
1556 cfmc      call readi(mcmcard,'MAXEVEN',maxeven,1000)
1557 cfmc      write(iout,*)'MAXEVEN=',maxeven
1558 cfmc      call readi(mcmcard,'MAXEVEN1',maxeven1,3)
1559 cfmc      write(iout,*)'MAXEVEN1=',maxeven1
1560 cfmc      call readi(mcmcard,'INIMIN',inimin,200)
1561 cfmc      write(iout,*)'INIMIN=',inimin
1562 cfmc      call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10)
1563 cfmc      write(iout,*)'NSTEPMCMF=',nstepmcmf
1564 cfmc      call readi(mcmcard,'NTHREAD',nthread,5)
1565 cfmc      write(iout,*)'NTHREAD=',nthread
1566 cfmc      call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500)
1567 cfmc      write(iout,*)'MAXSTEPMCMF=',maxstepmcmf
1568 cfmc      call readi(mcmcard,'MAXPERT',maxpert,9)
1569 cfmc      write(iout,*)'MAXPERT=',maxpert
1570 cfmc      call readi(mcmcard,'IRMSD',irmsd,1)
1571 cfmc      write(iout,*)'IRMSD=',irmsd
1572 cfmc      call reada(mcmcard,'DENEMIN',denemin,0.01D0)
1573 cfmc      write(iout,*)'DENEMIN=',denemin
1574 cfmc      call reada(mcmcard,'RCUT1S',rcut1s,3.5D0)
1575 cfmc      write(iout,*)'RCUT1S=',rcut1s
1576 cfmc      call reada(mcmcard,'RCUT1E',rcut1e,2.0D0)
1577 cfmc      write(iout,*)'RCUT1E=',rcut1e
1578 cfmc      call reada(mcmcard,'RCUT2S',rcut2s,0.5D0)
1579 cfmc      write(iout,*)'RCUT2S=',rcut2s
1580 cfmc      call reada(mcmcard,'RCUT2E',rcut2e,0.1D0)
1581 cfmc      write(iout,*)'RCUT2E=',rcut2e
1582 cfmc      call reada(mcmcard,'DPERT1',d_pert1,180.0D0)
1583 cfmc      write(iout,*)'DPERT1=',d_pert1
1584 cfmc      call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0)
1585 cfmc      write(iout,*)'DPERT1A=',d_pert1a
1586 cfmc      call reada(mcmcard,'DPERT2',d_pert2,90.0D0)
1587 cfmc      write(iout,*)'DPERT2=',d_pert2
1588 cfmc      call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0)
1589 cfmc      write(iout,*)'DPERT2A=',d_pert2a
1590 cfmc      call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0)
1591 cfmc      write(iout,*)'DPERT2B=',d_pert2b
1592 cfmc      call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0)
1593 cfmc      write(iout,*)'DPERT2C=',d_pert2c
1594 cfmc      d_pert1=deg2rad*d_pert1
1595 cfmc      d_pert1a=deg2rad*d_pert1a
1596 cfmc      d_pert2=deg2rad*d_pert2
1597 cfmc      d_pert2a=deg2rad*d_pert2a
1598 cfmc      d_pert2b=deg2rad*d_pert2b
1599 cfmc      d_pert2c=deg2rad*d_pert2c
1600 cfmc      call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0)
1601 cfmc      write(iout,*)'KT_MCMF1=',kt_mcmf1
1602 cfmc      call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0)
1603 cfmc      write(iout,*)'KT_MCMF2=',kt_mcmf2
1604 cfmc      call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0)
1605 cfmc      write(iout,*)'DKT_MCMF1=',dkt_mcmf1
1606 cfmc      call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0)
1607 cfmc      write(iout,*)'DKT_MCMF2=',dkt_mcmf2
1608 cfmc      call reada(mcmcard,'RCUTINI',rcutini,3.5D0)
1609 cfmc      write(iout,*)'RCUTINI=',rcutini
1610 cfmc      call reada(mcmcard,'GRAT',grat,0.5D0)
1611 cfmc      write(iout,*)'GRAT=',grat
1612 cfmc      call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0)
1613 cfmc      write(iout,*)'BIAS_MCMF=',bias_mcmf
1614 cfmc
1615 cfmc      return
1616 cfmc      end
1617 c----------------------------------------------------------------------------
1618       subroutine mcmread
1619       implicit real*8 (a-h,o-z)
1620       include 'DIMENSIONS'
1621       include 'COMMON.MCM'
1622       include 'COMMON.MCE'
1623       include 'COMMON.IOUNITS'
1624       character*80 ucase
1625       character*320 mcmcard
1626       call card_concat(mcmcard)
1627       call readi(mcmcard,'MAXACC',maxacc,100)
1628       call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
1629       call readi(mcmcard,'MAXTRIAL',maxtrial,100)
1630       call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
1631       call readi(mcmcard,'MAXREPM',maxrepm,200)
1632       call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
1633       call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
1634       call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
1635       call reada(mcmcard,'E_UP',e_up,5.0D0)
1636       call reada(mcmcard,'DELTE',delte,0.1D0)
1637       call readi(mcmcard,'NSWEEP',nsweep,5)
1638       call readi(mcmcard,'NSTEPH',nsteph,0)
1639       call readi(mcmcard,'NSTEPC',nstepc,0)
1640       call reada(mcmcard,'TMIN',tmin,298.0D0)
1641       call reada(mcmcard,'TMAX',tmax,298.0D0)
1642       call readi(mcmcard,'NWINDOW',nwindow,0)
1643       call readi(mcmcard,'PRINT_MC',print_mc,0)
1644       print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
1645       print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
1646       ent_read=(index(mcmcard,'ENT_READ').gt.0)
1647       call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
1648       call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
1649       call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
1650       call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
1651       call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
1652       if (nwindow.gt.0) then
1653         read (inp,*) (winstart(i),winend(i),i=1,nwindow)
1654         do i=1,nwindow
1655           winlen(i)=winend(i)-winstart(i)+1
1656         enddo
1657       endif
1658       if (tmax.lt.tmin) tmax=tmin
1659       if (tmax.eq.tmin) then
1660         nstepc=0
1661         nsteph=0
1662       endif
1663       if (nstepc.gt.0 .and. nsteph.gt.0) then
1664         tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
1665         tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
1666       endif
1667 C Probabilities of different move types
1668       sumpro_type(0)=0.0D0
1669       call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
1670       call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
1671       sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
1672       call reada(mcmcard,'THETA'     ,sumpro_type(3),0.0d0)
1673       sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
1674       call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
1675       sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
1676       do i=1,MaxMoveType
1677         print *,'i',i,' sumprotype',sumpro_type(i)
1678         sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
1679         print *,'i',i,' sumprotype',sumpro_type(i)
1680       enddo
1681       return
1682       end
1683 c----------------------------------------------------------------------------
1684       subroutine read_minim
1685       implicit real*8 (a-h,o-z)
1686       include 'DIMENSIONS'
1687       include 'COMMON.MINIM'
1688       include 'COMMON.IOUNITS'
1689       character*80 ucase
1690       character*320 minimcard
1691       call card_concat(minimcard)
1692       call readi(minimcard,'MAXMIN',maxmin,2000)
1693       call readi(minimcard,'MAXFUN',maxfun,5000)
1694       call readi(minimcard,'MINMIN',minmin,maxmin)
1695       call readi(minimcard,'MINFUN',minfun,maxmin)
1696       call reada(minimcard,'TOLF',tolf,1.0D-2)
1697       call reada(minimcard,'RTOLF',rtolf,1.0D-4)
1698       print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
1699       print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
1700       print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
1701       write (iout,'(/80(1h*)/20x,a/80(1h*))')
1702      &         'Options in energy minimization:'
1703       write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
1704      & 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
1705      & 'MinMin:',MinMin,' MinFun:',MinFun,
1706      & ' TolF:',TolF,' RTolF:',RTolF
1707       return
1708       end
1709 c----------------------------------------------------------------------------
1710       subroutine read_angles(kanal,*)
1711       implicit real*8 (a-h,o-z)
1712       include 'DIMENSIONS'
1713       include 'COMMON.GEO'
1714       include 'COMMON.VAR'
1715       include 'COMMON.CHAIN'
1716       include 'COMMON.IOUNITS'
1717       include 'COMMON.CONTROL'
1718 c Read angles from input
1719 c
1720        read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
1721        read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
1722        read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
1723        read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
1724
1725        do i=1,nres
1726 c 9/7/01 avoid 180 deg valence angle
1727         if (theta(i).gt.179.99d0) theta(i)=179.99d0
1728 c
1729         theta(i)=deg2rad*theta(i)
1730         phi(i)=deg2rad*phi(i)
1731         alph(i)=deg2rad*alph(i)
1732         omeg(i)=deg2rad*omeg(i)
1733        enddo
1734       return
1735    10 return1
1736       end
1737 c----------------------------------------------------------------------------
1738       subroutine reada(rekord,lancuch,wartosc,default)
1739       implicit none
1740       character*(*) rekord,lancuch
1741       double precision wartosc,default
1742       integer ilen,iread
1743       external ilen
1744       iread=index(rekord,lancuch)
1745       if (iread.eq.0) then
1746         wartosc=default
1747         return
1748       endif
1749       iread=iread+ilen(lancuch)+1
1750       read (rekord(iread:),*,err=10,end=10) wartosc
1751       return
1752   10  wartosc=default
1753       return
1754       end
1755 c----------------------------------------------------------------------------
1756       subroutine readi(rekord,lancuch,wartosc,default)
1757       implicit none
1758       character*(*) rekord,lancuch
1759       integer wartosc,default
1760       integer ilen,iread
1761       external ilen
1762       iread=index(rekord,lancuch)
1763       if (iread.eq.0) then
1764         wartosc=default
1765         return
1766       endif
1767       iread=iread+ilen(lancuch)+1
1768       read (rekord(iread:),*,err=10,end=10) wartosc
1769       return
1770   10  wartosc=default
1771       return
1772       end
1773 c----------------------------------------------------------------------------
1774       subroutine multreadi(rekord,lancuch,tablica,dim,default)
1775       implicit none
1776       integer dim,i
1777       integer tablica(dim),default
1778       character*(*) rekord,lancuch
1779       character*80 aux
1780       integer ilen,iread
1781       external ilen
1782       do i=1,dim
1783         tablica(i)=default
1784       enddo
1785       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1786       if (iread.eq.0) return
1787       iread=iread+ilen(lancuch)+1
1788       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1789    10 return
1790       end
1791 c----------------------------------------------------------------------------
1792       subroutine multreada(rekord,lancuch,tablica,dim,default)
1793       implicit none
1794       integer dim,i
1795       double precision tablica(dim),default
1796       character*(*) rekord,lancuch
1797       character*80 aux
1798       integer ilen,iread
1799       external ilen
1800       do i=1,dim
1801         tablica(i)=default
1802       enddo
1803       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1804       if (iread.eq.0) return
1805       iread=iread+ilen(lancuch)+1
1806       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1807    10 return
1808       end
1809 c----------------------------------------------------------------------------
1810       subroutine openunits
1811       implicit real*8 (a-h,o-z)
1812       include 'DIMENSIONS'
1813 #ifdef MPI
1814       include 'mpif.h'
1815       character*16 form,nodename
1816       integer nodelen
1817 #endif
1818       include 'COMMON.SETUP'
1819       include 'COMMON.IOUNITS'
1820       include 'COMMON.MD'
1821       include 'COMMON.CONTROL'
1822       integer lenpre,lenpot,ilen,lentmp
1823       external ilen
1824       character*3 out1file_text,ucase
1825       character*3 ll
1826       external ucase
1827 c      print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
1828       call getenv_loc("PREFIX",prefix)
1829       pref_orig = prefix
1830       call getenv_loc("POT",pot)
1831       call getenv_loc("DIRTMP",tmpdir)
1832       call getenv_loc("CURDIR",curdir)
1833       call getenv_loc("OUT1FILE",out1file_text)
1834 c      print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
1835       out1file_text=ucase(out1file_text)
1836       if (out1file_text(1:1).eq."Y") then
1837         out1file=.true.
1838       else
1839         out1file=fg_rank.gt.0
1840       endif
1841       lenpre=ilen(prefix)
1842       lenpot=ilen(pot)
1843       lentmp=ilen(tmpdir)
1844       if (lentmp.gt.0) then
1845           write (*,'(80(1h!))')
1846           write (*,'(a,19x,a,19x,a)') "!","  A T T E N T I O N  ","!"
1847           write (*,'(80(1h!))')
1848           write (*,*)"All output files will be on node /tmp directory."
1849 #ifdef MPI
1850         call  MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
1851         if (me.eq.king) then
1852           write (*,*) "The master node is ",nodename
1853         else if (fg_rank.eq.0) then
1854           write (*,*) "I am the CG slave node ",nodename
1855         else
1856           write (*,*) "I am the FG slave node ",nodename
1857         endif
1858 #endif
1859         PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
1860         lenpre = lentmp+lenpre+1
1861       endif
1862       entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
1863 C Get the names and open the input files
1864 #if defined(WINIFL) || defined(WINPGI)
1865       open(1,file=pref_orig(:ilen(pref_orig))//
1866      &  '.inp',status='old',readonly,shared)
1867        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1868 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1869 C Get parameter filenames and open the parameter files.
1870       call getenv_loc('BONDPAR',bondname)
1871       open (ibond,file=bondname,status='old',readonly,shared)
1872       call getenv_loc('THETPAR',thetname)
1873       open (ithep,file=thetname,status='old',readonly,shared)
1874       call getenv_loc('ROTPAR',rotname)
1875       open (irotam,file=rotname,status='old',readonly,shared)
1876       call getenv_loc('TORPAR',torname)
1877       open (itorp,file=torname,status='old',readonly,shared)
1878       call getenv_loc('TORDPAR',tordname)
1879       open (itordp,file=tordname,status='old',readonly,shared)
1880       call getenv_loc('FOURIER',fouriername)
1881       open (ifourier,file=fouriername,status='old',readonly,shared)
1882       call getenv_loc('ELEPAR',elename)
1883       open (ielep,file=elename,status='old',readonly,shared)
1884       call getenv_loc('SIDEPAR',sidename)
1885       open (isidep,file=sidename,status='old',readonly,shared)
1886 #elif (defined CRAY) || (defined AIX)
1887       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1888      &  action='read')
1889 c      print *,"Processor",myrank," opened file 1"
1890       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1891 c      print *,"Processor",myrank," opened file 9"
1892 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1893 C Get parameter filenames and open the parameter files.
1894       call getenv_loc('BONDPAR',bondname)
1895       open (ibond,file=bondname,status='old',action='read')
1896 c      print *,"Processor",myrank," opened file IBOND"
1897       call getenv_loc('THETPAR',thetname)
1898       open (ithep,file=thetname,status='old',action='read')
1899 c      print *,"Processor",myrank," opened file ITHEP"
1900       call getenv_loc('ROTPAR',rotname)
1901       open (irotam,file=rotname,status='old',action='read')
1902 c      print *,"Processor",myrank," opened file IROTAM"
1903       call getenv_loc('TORPAR',torname)
1904       open (itorp,file=torname,status='old',action='read')
1905 c      print *,"Processor",myrank," opened file ITORP"
1906       call getenv_loc('TORDPAR',tordname)
1907       open (itordp,file=tordname,status='old',action='read')
1908 c      print *,"Processor",myrank," opened file ITORDP"
1909       call getenv_loc('SCCORPAR',sccorname)
1910       open (isccor,file=sccorname,status='old',action='read')
1911 c      print *,"Processor",myrank," opened file ISCCOR"
1912       call getenv_loc('FOURIER',fouriername)
1913       open (ifourier,file=fouriername,status='old',action='read')
1914 c      print *,"Processor",myrank," opened file IFOURIER"
1915       call getenv_loc('ELEPAR',elename)
1916       open (ielep,file=elename,status='old',action='read')
1917 c      print *,"Processor",myrank," opened file IELEP"
1918       call getenv_loc('SIDEPAR',sidename)
1919       open (isidep,file=sidename,status='old',action='read')
1920 c      print *,"Processor",myrank," opened file ISIDEP"
1921 c      print *,"Processor",myrank," opened parameter files"
1922 #elif (defined G77)
1923       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
1924       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1925 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1926 C Get parameter filenames and open the parameter files.
1927       call getenv_loc('BONDPAR',bondname)
1928       open (ibond,file=bondname,status='old')
1929       call getenv_loc('THETPAR',thetname)
1930       open (ithep,file=thetname,status='old')
1931       call getenv_loc('ROTPAR',rotname)
1932       open (irotam,file=rotname,status='old')
1933       call getenv_loc('TORPAR',torname)
1934       open (itorp,file=torname,status='old')
1935       call getenv_loc('TORDPAR',tordname)
1936       open (itordp,file=tordname,status='old')
1937       call getenv_loc('SCCORPAR',sccorname)
1938       open (isccor,file=sccorname,status='old')
1939       call getenv_loc('FOURIER',fouriername)
1940       open (ifourier,file=fouriername,status='old')
1941       call getenv_loc('ELEPAR',elename)
1942       open (ielep,file=elename,status='old')
1943       call getenv_loc('SIDEPAR',sidename)
1944       open (isidep,file=sidename,status='old')
1945 #else
1946       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1947      &  readonly)
1948        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1949 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1950 C Get parameter filenames and open the parameter files.
1951       call getenv_loc('BONDPAR',bondname)
1952       open (ibond,file=bondname,status='old',readonly)
1953       call getenv_loc('THETPAR',thetname)
1954       open (ithep,file=thetname,status='old',readonly)
1955       call getenv_loc('ROTPAR',rotname)
1956       open (irotam,file=rotname,status='old',readonly)
1957       call getenv_loc('TORPAR',torname)
1958       open (itorp,file=torname,status='old',readonly)
1959       call getenv_loc('TORDPAR',tordname)
1960       open (itordp,file=tordname,status='old',readonly)
1961       call getenv_loc('SCCORPAR',sccorname)
1962       open (isccor,file=sccorname,status='old',readonly)
1963       call getenv_loc('FOURIER',fouriername)
1964       open (ifourier,file=fouriername,status='old',readonly)
1965       call getenv_loc('ELEPAR',elename)
1966       open (ielep,file=elename,status='old',readonly)
1967       call getenv_loc('SIDEPAR',sidename)
1968       open (isidep,file=sidename,status='old',readonly)
1969 #endif
1970 #ifndef OLDSCP
1971 C
1972 C 8/9/01 In the newest version SCp interaction constants are read from a file
1973 C Use -DOLDSCP to use hard-coded constants instead.
1974 C
1975       call getenv_loc('SCPPAR',scpname)
1976 #if defined(WINIFL) || defined(WINPGI)
1977       open (iscpp,file=scpname,status='old',readonly,shared)
1978 #elif (defined CRAY)  || (defined AIX)
1979       open (iscpp,file=scpname,status='old',action='read')
1980 #elif (defined G77)
1981       open (iscpp,file=scpname,status='old')
1982 #else
1983       open (iscpp,file=scpname,status='old',readonly)
1984 #endif
1985 #endif
1986       call getenv_loc('PATTERN',patname)
1987 #if defined(WINIFL) || defined(WINPGI)
1988       open (icbase,file=patname,status='old',readonly,shared)
1989 #elif (defined CRAY)  || (defined AIX)
1990       open (icbase,file=patname,status='old',action='read')
1991 #elif (defined G77)
1992       open (icbase,file=patname,status='old')
1993 #else
1994       open (icbase,file=patname,status='old',readonly)
1995 #endif
1996 #ifdef MPI
1997 C Open output file only for CG processes
1998 c      print *,"Processor",myrank," fg_rank",fg_rank
1999       if (fg_rank.eq.0) then
2000
2001       if (nodes.eq.1) then
2002         npos=3
2003       else
2004         npos = dlog10(dfloat(nodes-1))+1
2005       endif
2006       if (npos.lt.3) npos=3
2007       write (liczba,'(i1)') npos
2008       form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
2009      &  //')'
2010       write (liczba,form) me
2011       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//
2012      &  liczba(:ilen(liczba))
2013       intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2014      &  //'.int'
2015       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2016      &  //'.pdb'
2017       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
2018      &  liczba(:ilen(liczba))//'.mol2'
2019       statname=prefix(:lenpre)//'_'//pot(:lenpot)//
2020      &  liczba(:ilen(liczba))//'.stat'
2021       if (lentmp.gt.0)
2022      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2023      &      //liczba(:ilen(liczba))//'.stat')
2024       rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba))
2025      &  //'.rst'
2026       if(usampl) then
2027           qname=prefix(:lenpre)//'_'//pot(:lenpot)//
2028      & liczba(:ilen(liczba))//'.const'
2029       endif
2030
2031       endif
2032 #else
2033       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
2034       intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
2035       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
2036       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
2037       statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
2038       if (lentmp.gt.0)
2039      &  call copy_to_tmp(pref_orig(:ile(pref_orig))//'_'//pot(:lenpot)//
2040      &    //'.stat')
2041       rest2name=prefix(:ilen(prefix))//'.rst'
2042       if(usampl) then
2043          qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
2044       endif
2045 #endif
2046 #if defined(AIX) || defined(PGI)
2047       if (me.eq.king .or. .not. out1file)
2048      &   open(iout,file=outname,status='unknown')
2049 #ifdef DEBUG
2050       if (fg_rank.gt.0) then
2051         write (liczba,'(i3.3)') myrank/nfgtasks
2052         write (ll,'(bz,i3.3)') fg_rank
2053         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2054      &   status='unknown')
2055       endif
2056 #endif
2057       if(me.eq.king) then
2058        open(igeom,file=intname,status='unknown',position='append')
2059        open(ipdb,file=pdbname,status='unknown')
2060        open(imol2,file=mol2name,status='unknown')
2061        open(istat,file=statname,status='unknown',position='append')
2062       else
2063 c1out       open(iout,file=outname,status='unknown')
2064       endif
2065 #else
2066       if (me.eq.king .or. .not.out1file)
2067      &    open(iout,file=outname,status='unknown')
2068 #ifdef DEBUG
2069       if (fg_rank.gt.0) then
2070         write (liczba,'(i3.3)') myrank/nfgtasks
2071         write (ll,'(bz,i3.3)') fg_rank
2072         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2073      &   status='unknown')
2074       endif
2075 #endif
2076       if(me.eq.king) then
2077        open(igeom,file=intname,status='unknown',access='append')
2078        open(ipdb,file=pdbname,status='unknown')
2079        open(imol2,file=mol2name,status='unknown')
2080        open(istat,file=statname,status='unknown',access='append')
2081       else
2082 c1out       open(iout,file=outname,status='unknown')
2083       endif
2084 #endif
2085       csa_rbank=prefix(:lenpre)//'.CSA.rbank'
2086       csa_seed=prefix(:lenpre)//'.CSA.seed'
2087       csa_history=prefix(:lenpre)//'.CSA.history'
2088       csa_bank=prefix(:lenpre)//'.CSA.bank'
2089       csa_bank1=prefix(:lenpre)//'.CSA.bank1'
2090       csa_alpha=prefix(:lenpre)//'.CSA.alpha'
2091       csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
2092 c!bankt      csa_bankt=prefix(:lenpre)//'.CSA.bankt'
2093       csa_int=prefix(:lenpre)//'.int'
2094       csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
2095       csa_native_int=prefix(:lenpre)//'.CSA.native.int'
2096       csa_in=prefix(:lenpre)//'.CSA.in'
2097 c      print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
2098 C Write file names
2099       if (me.eq.king)then
2100       write (iout,'(80(1h-))')
2101       write (iout,'(30x,a)') "FILE ASSIGNMENT"
2102       write (iout,'(80(1h-))')
2103       write (iout,*) "Input file                      : ",
2104      &  pref_orig(:ilen(pref_orig))//'.inp'
2105       write (iout,*) "Output file                     : ",
2106      &  outname(:ilen(outname))
2107       write (iout,*)
2108       write (iout,*) "Sidechain potential file        : ",
2109      &  sidename(:ilen(sidename))
2110 #ifndef OLDSCP
2111       write (iout,*) "SCp potential file              : ",
2112      &  scpname(:ilen(scpname))
2113 #endif
2114       write (iout,*) "Electrostatic potential file    : ",
2115      &  elename(:ilen(elename))
2116       write (iout,*) "Cumulant coefficient file       : ",
2117      &  fouriername(:ilen(fouriername))
2118       write (iout,*) "Torsional parameter file        : ",
2119      &  torname(:ilen(torname))
2120       write (iout,*) "Double torsional parameter file : ",
2121      &  tordname(:ilen(tordname))
2122       write (iout,*) "SCCOR parameter file : ",
2123      &  sccorname(:ilen(sccorname))
2124       write (iout,*) "Bond & inertia constant file    : ",
2125      &  bondname(:ilen(bondname))
2126       write (iout,*) "Bending parameter file          : ",
2127      &  thetname(:ilen(thetname))
2128       write (iout,*) "Rotamer parameter file          : ",
2129      &  rotname(:ilen(rotname))
2130       write (iout,*) "Threading database              : ",
2131      &  patname(:ilen(patname))
2132       if (lentmp.ne.0)
2133      &write (iout,*)" DIRTMP                          : ",
2134      &  tmpdir(:lentmp)
2135       write (iout,'(80(1h-))')
2136       endif
2137       return
2138       end
2139 c----------------------------------------------------------------------------
2140       subroutine card_concat(card)
2141       implicit real*8 (a-h,o-z)
2142       include 'DIMENSIONS'
2143       include 'COMMON.IOUNITS'
2144       character*(*) card
2145       character*80 karta,ucase
2146       external ilen
2147       read (inp,'(a)') karta
2148       karta=ucase(karta)
2149       card=' '
2150       do while (karta(80:80).eq.'&')
2151         card=card(:ilen(card)+1)//karta(:79)
2152         read (inp,'(a)') karta
2153         karta=ucase(karta)
2154       enddo
2155       card=card(:ilen(card)+1)//karta
2156       return
2157       end
2158 c----------------------------------------------------------------------------------
2159       subroutine readrst
2160       implicit real*8 (a-h,o-z)
2161       include 'DIMENSIONS'
2162       include 'COMMON.CHAIN'
2163       include 'COMMON.IOUNITS'
2164       include 'COMMON.MD'
2165       open(irest2,file=rest2name,status='unknown')
2166       read(irest2,*) totT,EK,potE,totE,t_bath
2167       do i=1,2*nres
2168          read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
2169       enddo
2170       do i=1,2*nres
2171          read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
2172       enddo
2173       if(usampl) then
2174              read (irest2,*) iset
2175       endif
2176       close(irest2)
2177       return
2178       end
2179 c---------------------------------------------------------------------------------
2180       subroutine read_fragments
2181       implicit real*8 (a-h,o-z)
2182       include 'DIMENSIONS'
2183 #ifdef MPI
2184       include 'mpif.h'
2185 #endif
2186       include 'COMMON.SETUP'
2187       include 'COMMON.CHAIN'
2188       include 'COMMON.IOUNITS'
2189       include 'COMMON.MD'
2190       include 'COMMON.CONTROL'
2191       read(inp,*) nset,nfrag,npair,nfrag_back
2192       if(me.eq.king.or..not.out1file)
2193      & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
2194      &  " nfrag_back",nfrag_back
2195       do iset=1,nset
2196          read(inp,*) mset(iset)
2197        do i=1,nfrag
2198          read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
2199      &     qinfrag(i,iset)
2200          if(me.eq.king.or..not.out1file)
2201      &    write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
2202      &     ifrag(2,i,iset), qinfrag(i,iset)
2203        enddo
2204        do i=1,npair
2205         read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
2206      &    qinpair(i,iset)
2207         if(me.eq.king.or..not.out1file)
2208      &   write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
2209      &    ipair(2,i,iset), qinpair(i,iset)
2210        enddo
2211        do i=1,nfrag_back
2212         read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2213      &     wfrag_back(3,i,iset),
2214      &     ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2215         if(me.eq.king.or..not.out1file)
2216      &   write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2217      &   wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2218        enddo
2219       enddo
2220       return
2221       end
2222 c-------------------------------------------------------------------------------
2223       subroutine read_dist_constr
2224       implicit real*8 (a-h,o-z)
2225       include 'DIMENSIONS'
2226 #ifdef MPI
2227       include 'mpif.h'
2228 #endif
2229       include 'COMMON.SETUP'
2230       include 'COMMON.CONTROL'
2231       include 'COMMON.CHAIN'
2232       include 'COMMON.IOUNITS'
2233       include 'COMMON.SBRIDGE'
2234       integer ifrag_(2,100),ipair_(2,100)
2235       double precision wfrag_(100),wpair_(100)
2236       character*500 controlcard
2237 c      write (iout,*) "Calling read_dist_constr"
2238 c      write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
2239 c      call flush(iout)
2240       call card_concat(controlcard)
2241       call readi(controlcard,"NFRAG",nfrag_,0)
2242       call readi(controlcard,"NPAIR",npair_,0)
2243       call readi(controlcard,"NDIST",ndist_,0)
2244       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
2245       call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
2246       call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
2247       call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
2248       call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
2249 c      write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
2250 c      write (iout,*) "IFRAG"
2251 c      do i=1,nfrag_
2252 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2253 c      enddo
2254 c      write (iout,*) "IPAIR"
2255 c      do i=1,npair_
2256 c        write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
2257 c      enddo
2258       call flush(iout)
2259       do i=1,nfrag_
2260         if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
2261         if (ifrag_(2,i).gt.nstart_sup+nsup-1)
2262      &    ifrag_(2,i)=nstart_sup+nsup-1
2263 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2264         call flush(iout)
2265         if (wfrag_(i).gt.0.0d0) then
2266         do j=ifrag_(1,i),ifrag_(2,i)-1
2267           do k=j+1,ifrag_(2,i)
2268 c            write (iout,*) "j",j," k",k
2269             ddjk=dist(j,k)
2270             if (constr_dist.eq.1) then
2271             nhpb=nhpb+1
2272             ihpb(nhpb)=j
2273             jhpb(nhpb)=k
2274               dhpb(nhpb)=ddjk
2275             forcon(nhpb)=wfrag_(i)
2276             else if (constr_dist.eq.2) then
2277               if (ddjk.le.dist_cut) then
2278                 nhpb=nhpb+1
2279                 ihpb(nhpb)=j
2280                 jhpb(nhpb)=k
2281                 dhpb(nhpb)=ddjk
2282                 forcon(nhpb)=wfrag_(i)
2283               endif
2284             else
2285               nhpb=nhpb+1
2286               ihpb(nhpb)=j
2287               jhpb(nhpb)=k
2288               dhpb(nhpb)=ddjk
2289               forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
2290             endif
2291 #ifdef MPI
2292             if (.not.out1file .or. me.eq.king)
2293      &      write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2294      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2295 #else
2296             write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2297      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2298 #endif
2299           enddo
2300         enddo
2301         endif
2302       enddo
2303       do i=1,npair_
2304         if (wpair_(i).gt.0.0d0) then
2305         ii = ipair_(1,i)
2306         jj = ipair_(2,i)
2307         if (ii.gt.jj) then
2308           itemp=ii
2309           ii=jj
2310           jj=itemp
2311         endif
2312         do j=ifrag_(1,ii),ifrag_(2,ii)
2313           do k=ifrag_(1,jj),ifrag_(2,jj)
2314             nhpb=nhpb+1
2315             ihpb(nhpb)=j
2316             jhpb(nhpb)=k
2317             forcon(nhpb)=wpair_(i)
2318             dhpb(nhpb)=dist(j,k)
2319 #ifdef MPI
2320             if (.not.out1file .or. me.eq.king)
2321      &      write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2322      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2323 #else
2324             write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2325      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2326 #endif
2327           enddo
2328         enddo
2329         endif
2330       enddo
2331       do i=1,ndist_
2332         read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
2333         if (forcon(nhpb+1).gt.0.0d0) then
2334           nhpb=nhpb+1
2335           dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
2336 #ifdef MPI
2337           if (.not.out1file .or. me.eq.king)
2338      &    write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2339      &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2340 #else
2341           write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2342      &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2343 #endif
2344         endif
2345       enddo
2346       call flush(iout)
2347       return
2348       end
2349 c-------------------------------------------------------------------------------
2350 #ifdef WINIFL
2351       subroutine flush(iu)
2352       return
2353       end
2354 #endif
2355 #ifdef AIX
2356       subroutine flush(iu)
2357       call flush_(iu)
2358       return
2359       end
2360 #endif
2361 c------------------------------------------------------------------------------
2362       subroutine copy_to_tmp(source)
2363       include "DIMENSIONS"
2364       include "COMMON.IOUNITS"
2365       character*(*) source
2366       character* 256 tmpfile
2367       integer ilen
2368       external ilen
2369       logical ex
2370       tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source))
2371       inquire(file=tmpfile,exist=ex)
2372       if (ex) then
2373         write (*,*) "Copying ",tmpfile(:ilen(tmpfile)),
2374      &   " to temporary directory..."
2375         write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir
2376         call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir)
2377       endif
2378       return
2379       end
2380 c------------------------------------------------------------------------------
2381       subroutine move_from_tmp(source)
2382       include "DIMENSIONS"
2383       include "COMMON.IOUNITS"
2384       character*(*) source
2385       integer ilen
2386       external ilen
2387       write (*,*) "Moving ",source(:ilen(source)),
2388      & " from temporary directory to working directory"
2389       write (*,*) "/bin/mv "//source(:ilen(source))//" "//curdir
2390       call system("/bin/mv "//source(:ilen(source))//" "//curdir)
2391       return
2392       end
2393 c------------------------------------------------------------------------------
2394       subroutine random_init(seed)
2395 C
2396 C Initialize random number generator
2397 C
2398       implicit real*8 (a-h,o-z)
2399       include 'DIMENSIONS'
2400 #ifdef MPI
2401       include 'mpif.h'
2402       logical OKRandom, prng_restart
2403       real*8  r1
2404       integer iseed_array(4)
2405 #endif
2406       include 'COMMON.IOUNITS'
2407       include 'COMMON.TIME1'
2408       include 'COMMON.THREAD'
2409       include 'COMMON.SBRIDGE'
2410       include 'COMMON.CONTROL'
2411       include 'COMMON.MCM'
2412       include 'COMMON.MAP'
2413       include 'COMMON.HEADER'
2414       include 'COMMON.CSA'
2415       include 'COMMON.CHAIN'
2416       include 'COMMON.MUCA'
2417       include 'COMMON.MD'
2418       include 'COMMON.FFIELD'
2419       include 'COMMON.SETUP'
2420       iseed=-dint(dabs(seed))
2421       if (iseed.eq.0) then
2422         write (iout,'(/80(1h*)/20x,a/80(1h*))')
2423      &    'Random seed undefined. The program will stop.'
2424         write (*,'(/80(1h*)/20x,a/80(1h*))')
2425      &    'Random seed undefined. The program will stop.'
2426 #ifdef MPI
2427         call mpi_finalize(mpi_comm_world,ierr)
2428 #endif
2429         stop 'Bad random seed.'
2430       endif
2431 #ifdef MPI
2432       if (fg_rank.eq.0) then
2433       seed=seed*(me+1)+1
2434 #ifdef AMD64
2435       if(me.eq.king)
2436      &  write (iout,*) 'MPI: node= ', me, ' iseed= ',iseed
2437       OKRandom = prng_restart(me,iseed)
2438 #else
2439       do i=1,4
2440        tmp=65536.0d0**(4-i)
2441        iseed_array(i) = dint(seed/tmp)
2442        seed=seed-iseed_array(i)*tmp
2443       enddo
2444       if(me.eq.king)
2445      & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ',
2446      &                 (iseed_array(i),i=1,4)
2447       write (*,*) 'MPI: node= ',me, ' iseed(4)= ',
2448      &                 (iseed_array(i),i=1,4)
2449       OKRandom = prng_restart(me,iseed_array)
2450 #endif
2451       if (OKRandom) then
2452 c        r1 = prng_next(me)
2453         r1=ran_number(0.0D0,1.0D0)
2454         if(me.eq.king)
2455      &   write (iout,*) 'ran_num',r1
2456         if (r1.lt.0.0d0) OKRandom=.false.
2457       endif
2458       if (.not.OKRandom) then
2459         write (iout,*) 'PRNG IS NOT WORKING!!!'
2460         print *,'PRNG IS NOT WORKING!!!'
2461         if (me.eq.0) then
2462          call flush(iout)
2463          call mpi_abort(mpi_comm_world,error_msg,ierr)
2464          stop
2465         else
2466          write (iout,*) 'too many processors for parallel prng'
2467          write (*,*) 'too many processors for parallel prng'
2468          call flush(iout)
2469          stop
2470         endif
2471       endif
2472       endif
2473 #else
2474       call vrndst(iseed)
2475       write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0)
2476 #endif
2477       return
2478       end