source/unres/src_MD/readrtns.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 csa      if (modecalc.eq.8) then
  32 csa       inquire (file="fort.40",exist=file_exist)
  33 csa       if (.not.file_exist) call csaread
  34 csa      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,i2,3f10.5)') i-nss,ihpb(i),jhpb(i),
  48      &     ibecarb(i),dhpb(i),dhpb1(i),forcon(i)
  49       enddo
  50 #ifdef MPI
  51       endif
  52 #endif
  53 c      print *,"Processor",myrank," leaves READRTNS"
  54       return
  55       end
  56 C-------------------------------------------------------------------------------
  57       subroutine read_control
  58 C
  59 C Read contorl data
  60 C
  61       implicit real*8 (a-h,o-z)
  62       include 'DIMENSIONS'
  63 #ifdef MP
  64       include 'mpif.h'
  65       logical OKRandom, prng_restart
  66       real*8  r1
  67 #endif
  68       include 'COMMON.IOUNITS'
  69       include 'COMMON.TIME1'
  70       include 'COMMON.THREAD'
  71       include 'COMMON.SBRIDGE'
  72       include 'COMMON.CONTROL'
  73       include 'COMMON.MCM'
  74       include 'COMMON.MAP'
  75       include 'COMMON.HEADER'
  76 csa      include 'COMMON.CSA'
  77       include 'COMMON.CHAIN'
  78       include 'COMMON.MUCA'
  79       include 'COMMON.MD'
  80       include 'COMMON.FFIELD'
  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 reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
 100       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
 101       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
 102       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
 103       call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
 104       call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
 105       call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
 106       call reada(controlcard,'DRMS',drms,0.1D0)
 107       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
 108        write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
 109        write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
 110        write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
 111        write (iout,'(a,f10.1)')'DRMS    = ',drms
 112        write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
 113        write (iout,'(a,f10.1)') 'Time limit (min):',timlim
 114       endif
 115       call readi(controlcard,'NZ_START',nz_start,0)
 116       call readi(controlcard,'NZ_END',nz_end,0)
 117       call readi(controlcard,'IZ_SC',iz_sc,0)
 118       timlim=60.0D0*timlim
 119       safety = 60.0d0*safety
 120       timem=timlim
 121       modecalc=0
 122       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 123       minim=(index(controlcard,'MINIMIZE').gt.0)
 124       dccart=(index(controlcard,'CART').gt.0)
 125       overlapsc=(index(controlcard,'OVERLAP').gt.0)
 126       overlapsc=.not.overlapsc
 127       searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
 128       searchsc=.not.searchsc
 129       sideadd=(index(controlcard,'SIDEADD').gt.0)
 130       energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
 131       outpdb=(index(controlcard,'PDBOUT').gt.0)
 132       outmol2=(index(controlcard,'MOL2OUT').gt.0)
 133       pdbref=(index(controlcard,'PDBREF').gt.0)
 134       refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
 135       indpdb=index(controlcard,'PDBSTART')
 136       extconf=(index(controlcard,'EXTCONF').gt.0)
 137       call readi(controlcard,'IPRINT',iprint,0)
 138       call readi(controlcard,'MAXGEN',maxgen,10000)
 139       call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
 140       call readi(controlcard,"KDIAG",kdiag,0)
 141       call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
 142       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
 143      & write (iout,*) "RESCALE_MODE",rescale_mode
 144       split_ene=index(controlcard,'SPLIT_ENE').gt.0
 145       if (index(controlcard,'REGULAR').gt.0.0D0) then
 146         call reada(controlcard,'WEIDIS',weidis,0.1D0)
 147         modecalc=1
 148         refstr=.true.
 149       endif
 150       if (index(controlcard,'CHECKGRAD').gt.0) then
 151         modecalc=5
 152         if (index(controlcard,'CART').gt.0) then
 153           icheckgrad=1
 154         elseif (index(controlcard,'CARINT').gt.0) then
 155           icheckgrad=2
 156         else
 157           icheckgrad=3
 158         endif
 159       elseif (index(controlcard,'THREAD').gt.0) then
 160         modecalc=2
 161         call readi(controlcard,'THREAD',nthread,0)
 162         if (nthread.gt.0) then
 163           call reada(controlcard,'WEIDIS',weidis,0.1D0)
 164         else
 165           if (fg_rank.eq.0)
 166      &    write (iout,'(a)')'A number has to follow the THREAD keyword.'
 167           stop 'Error termination in Read_Control.'
 168         endif
 169       else if (index(controlcard,'MCMA').gt.0) then
 170         modecalc=3
 171       else if (index(controlcard,'MCEE').gt.0) then
 172         modecalc=6
 173       else if (index(controlcard,'MULTCONF').gt.0) then
 174         modecalc=4
 175       else if (index(controlcard,'MAP').gt.0) then
 176         modecalc=7
 177         call readi(controlcard,'MAP',nmap,0)
 178       else if (index(controlcard,'CSA').gt.0) then
 179            write(*,*) "CSA not supported in this version"
 180            stop
 181 csa        modecalc=8
 182 crc      else if (index(controlcard,'ZSCORE').gt.0) then
 183 crc
 184 crc  ZSCORE is rm from UNRES, modecalc=9 is available
 185 crc
 186 crc        modecalc=9
 187 cfcm      else if (index(controlcard,'MCMF').gt.0) then
 188 cfmc        modecalc=10
 189       else if (index(controlcard,'SOFTREG').gt.0) then
 190         modecalc=11
 191       else if (index(controlcard,'CHECK_BOND').gt.0) then
 192         modecalc=-1
 193       else if (index(controlcard,'TEST').gt.0) then
 194         modecalc=-2
 195       else if (index(controlcard,'MD').gt.0) then
 196         modecalc=12
 197       else if (index(controlcard,'RE ').gt.0) then
 198         modecalc=14
 199       endif
 200
 201       lmuca=index(controlcard,'MUCA').gt.0
 202       call readi(controlcard,'MUCADYN',mucadyn,0)
 203       call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
 204       if (lmuca .and. (me.eq.king .or. .not.out1file ))
 205      & then
 206        write (iout,*) 'MUCADYN=',mucadyn
 207        write (iout,*) 'MUCASMOOTH=',muca_smooth
 208       endif
 209
 210       iscode=index(controlcard,'ONE_LETTER')
 211       indphi=index(controlcard,'PHI')
 212       indback=index(controlcard,'BACK')
 213       iranconf=index(controlcard,'RAND_CONF')
 214       i2ndstr=index(controlcard,'USE_SEC_PRED')
 215       gradout=index(controlcard,'GRADOUT').gt.0
 216       gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
 217
 218       if(me.eq.king.or..not.out1file)
 219      & write (iout,'(2a)') diagmeth(kdiag),
 220      &  ' routine used to diagonalize matrices.'
 221       return
 222       end
 223 c--------------------------------------------------------------------------
 224       subroutine read_REMDpar
 225 C
 226 C Read REMD settings
 227 C
 228       implicit real*8 (a-h,o-z)
 229       include 'DIMENSIONS'
 230       include 'COMMON.IOUNITS'
 231       include 'COMMON.TIME1'
 232       include 'COMMON.MD'
 233 #ifndef LANG0
 234       include 'COMMON.LANGEVIN'
 235 #else
 236       include 'COMMON.LANGEVIN.lang0'
 237 #endif
 238       include 'COMMON.INTERACT'
 239       include 'COMMON.NAMES'
 240       include 'COMMON.GEO'
 241       include 'COMMON.REMD'
 242       include 'COMMON.CONTROL'
 243       include 'COMMON.SETUP'
 244       character*80 ucase
 245       character*320 controlcard
 246       character*3200 controlcard1
 247       integer iremd_m_total
 248
 249       if(me.eq.king.or..not.out1file)
 250      & write (iout,*) "REMD setup"
 251
 252       call card_concat(controlcard)
 253       call readi(controlcard,"NREP",nrep,3)
 254       call readi(controlcard,"NSTEX",nstex,1000)
 255       call reada(controlcard,"RETMIN",retmin,10.0d0)
 256       call reada(controlcard,"RETMAX",retmax,1000.0d0)
 257       mremdsync=(index(controlcard,'SYNC').gt.0)
 258       call readi(controlcard,"NSYN",i_sync_step,100)
 259       restart1file=(index(controlcard,'REST1FILE').gt.0)
 260       traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
 261       call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
 262       if(max_cache_traj_use.gt.max_cache_traj)
 263      &           max_cache_traj_use=max_cache_traj
 264       if(me.eq.king.or..not.out1file) then
 265 cd       if (traj1file) then
 266 crc caching is in testing - NTWX is not ignored
 267 cd        write (iout,*) "NTWX value is ignored"
 268 cd        write (iout,*) "  trajectory is stored to one file by master"
 269 cd        write (iout,*) "  before exchange at NSTEX intervals"
 270 cd       endif
 271        write (iout,*) "NREP= ",nrep
 272        write (iout,*) "NSTEX= ",nstex
 273        write (iout,*) "SYNC= ",mremdsync
 274        write (iout,*) "NSYN= ",i_sync_step
 275        write (iout,*) "TRAJCACHE= ",max_cache_traj_use
 276       endif
 277
 278       t_exchange_only=(index(controlcard,'TONLY').gt.0)
 279       call readi(controlcard,"HREMD",hremd,0)
 280       if((me.eq.king.or..not.out1file).and.hremd.gt.0) then
 281         write (iout,*) "Hamiltonian REMD with ",hremd," sets of weights"
 282       endif
 283       if(usampl.and.hremd.gt.0) then
 284             write (iout,'(//a)')
 285      &      "========== ERROR: USAMPL and HREMD cannot be used together"
 286 #ifdef MPI
 287             call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
 288 #endif
 289             stop
 290       endif
 291
 292
 293       remd_tlist=.false.
 294       if (index(controlcard,'TLIST').gt.0) then
 295          remd_tlist=.true.
 296          call card_concat(controlcard1)
 297          read(controlcard1,*) (remd_t(i),i=1,nrep)
 298          if(me.eq.king.or..not.out1file)
 299      &    write (iout,*)'tlist',(remd_t(i),i=1,nrep)
 300       endif
 301       remd_mlist=.false.
 302       if (index(controlcard,'MLIST').gt.0) then
 303          remd_mlist=.true.
 304          call card_concat(controlcard1)
 305          read(controlcard1,*) (remd_m(i),i=1,nrep)
 306          if(me.eq.king.or..not.out1file) then
 307           write (iout,*)'mlist',(remd_m(i),i=1,nrep)
 308           iremd_m_total=0
 309           do i=1,nrep
 310            iremd_m_total=iremd_m_total+remd_m(i)
 311           enddo
 312           if(hremd.gt.1)then
 313            write (iout,*) 'Total number of replicas ',
 314      &       iremd_m_total*hremd
 315           else
 316            write (iout,*) 'Total number of replicas ',iremd_m_total
 317           endif
 318          endif
 319       endif
 320       if(me.eq.king.or..not.out1file)
 321      &   write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
 322       return
 323       end
 324 c--------------------------------------------------------------------------
 325       subroutine read_MDpar
 326 C
 327 C Read MD settings
 328 C
 329       implicit real*8 (a-h,o-z)
 330       include 'DIMENSIONS'
 331       include 'COMMON.IOUNITS'
 332       include 'COMMON.TIME1'
 333       include 'COMMON.MD'
 334 #ifndef LANG0
 335       include 'COMMON.LANGEVIN'
 336 #else
 337       include 'COMMON.LANGEVIN.lang0'
 338 #endif
 339       include 'COMMON.INTERACT'
 340       include 'COMMON.NAMES'
 341       include 'COMMON.GEO'
 342       include 'COMMON.SETUP'
 343       include 'COMMON.CONTROL'
 344       include 'COMMON.SPLITELE'
 345       character*80 ucase
 346       character*320 controlcard
 347
 348       call card_concat(controlcard)
 349       call readi(controlcard,"NSTEP",n_timestep,1000000)
 350       call readi(controlcard,"NTWE",ntwe,100)
 351       call readi(controlcard,"NTWX",ntwx,1000)
 352       call reada(controlcard,"DT",d_time,1.0d-1)
 353       call reada(controlcard,"DVMAX",dvmax,2.0d1)
 354       call reada(controlcard,"DAMAX",damax,1.0d1)
 355       call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
 356       call readi(controlcard,"LANG",lang,0)
 357       RESPA = index(controlcard,"RESPA") .gt. 0
 358       call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
 359       ntime_split0=ntime_split
 360       call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
 361       ntime_split0=ntime_split
 362       call reada(controlcard,"R_CUT",r_cut,2.0d0)
 363       call reada(controlcard,"LAMBDA",rlamb,0.3d0)
 364       rest = index(controlcard,"REST").gt.0
 365       tbf = index(controlcard,"TBF").gt.0
 366       call readi(controlcard,"HMC",hmc,0)
 367       tnp = index(controlcard,"NOSEPOINCARE99").gt.0
 368       tnp1 = index(controlcard,"NOSEPOINCARE01").gt.0
 369       tnh = index(controlcard,"NOSEHOOVER96").gt.0
 370       if (RESPA.and.tnh)then
 371         xiresp = index(controlcard,"XIRESP").gt.0
 372       endif
 373       call reada(controlcard,"Q_NP",Q_np,0.1d0)
 374       usampl = index(controlcard,"USAMPL").gt.0
 375
 376       mdpdb = index(controlcard,"MDPDB").gt.0
 377       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 378       call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
 379       call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
 380       call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
 381       if (count_reset_moment.eq.0) count_reset_moment=1000000000
 382       call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
 383       reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
 384       reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
 385       if (count_reset_vel.eq.0) count_reset_vel=1000000000
 386       large = index(controlcard,"LARGE").gt.0
 387       print_compon = index(controlcard,"PRINT_COMPON").gt.0
 388       rattle = index(controlcard,"RATTLE").gt.0
 389 c  if performing umbrella sampling, fragments constrained are read from the fragment file
 390       nset=0
 391       if(usampl) then
 392         call read_fragments
 393       endif
 394
 395       if(me.eq.king.or..not.out1file) then
 396        write (iout,*)
 397        write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
 398        write (iout,*)
 399        write (iout,'(a)') "The units are:"
 400        write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
 401        write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",
 402      &  " acceleration: angstrom/(48.9 fs)**2"
 403        write (iout,'(a)') "energy: kcal/mol, temperature: K"
 404        write (iout,*)
 405        write (iout,'(a60,i10)') "Number of time steps:",n_timestep
 406        write (iout,'(a60,f10.5,a)')
 407      &  "Initial time step of numerical integration:",d_time,
 408      &  " natural units"
 409        write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
 410        if (RESPA) then
 411         write (iout,'(2a,i4,a)')
 412      &    "A-MTS algorithm used; initial time step for fast-varying",
 413      &    " short-range forces split into",ntime_split," steps."
 414         write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
 415      &   r_cut," lambda",rlamb
 416        endif
 417        write (iout,'(2a,f10.5)')
 418      &  "Maximum acceleration threshold to reduce the time step",
 419      &  "/increase split number:",damax
 420        write (iout,'(2a,f10.5)')
 421      &  "Maximum predicted energy drift to reduce the timestep",
 422      &  "/increase split number:",edriftmax
 423        write (iout,'(a60,f10.5)')
 424      & "Maximum velocity threshold to reduce velocities:",dvmax
 425        write (iout,'(a60,i10)') "Frequency of property output:",ntwe
 426        write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
 427        if (rattle) write (iout,'(a60)')
 428      &  "Rattle algorithm used to constrain the virtual bonds"
 429       endif
 430       reset_fricmat=1000
 431       if (lang.gt.0) then
 432         call reada(controlcard,"ETAWAT",etawat,0.8904d0)
 433         call reada(controlcard,"RWAT",rwat,1.4d0)
 434         call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
 435         surfarea=index(controlcard,"SURFAREA").gt.0
 436         call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
 437         if(me.eq.king.or..not.out1file)then
 438          write (iout,'(/a,$)') "Langevin dynamics calculation"
 439          if (lang.eq.1) then
 440           write (iout,'(a/)')
 441      &      " with direct integration of Langevin equations"
 442          else if (lang.eq.2) then
 443           write (iout,'(a/)') " with TINKER stochasic MD integrator"
 444          else if (lang.eq.3) then
 445           write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
 446          else if (lang.eq.4) then
 447           write (iout,'(a/)') " in overdamped mode"
 448          else
 449           write (iout,'(//a,i5)')
 450      &      "=========== ERROR: Unknown Langevin dynamics mode:",lang
 451           stop
 452          endif
 453          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 454          write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
 455          write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
 456          write (iout,'(a60,f10.5)')
 457      &   "Scaling factor of the friction forces:",scal_fric
 458          if (surfarea) write (iout,'(2a,i10,a)')
 459      &     "Friction coefficients will be scaled by solvent-accessible",
 460      &     " surface area every",reset_fricmat," steps."
 461         endif
 462 c Calculate friction coefficients and bounds of stochastic forces
 463         eta=6*pi*cPoise*etawat
 464         if(me.eq.king.or..not.out1file)
 465      &   write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:"
 466      &   ,eta
 467         gamp=scal_fric*(pstok+rwat)*eta
 468         stdfp=dsqrt(2*Rb*t_bath/d_time)
 469         do i=1,ntyp
 470           gamsc(i)=scal_fric*(restok(i)+rwat)*eta
 471           stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
 472         enddo
 473         if(me.eq.king.or..not.out1file)then
 474          write (iout,'(/2a/)')
 475      &   "Radii of site types and friction coefficients and std's of",
 476      &   " stochastic forces of fully exposed sites"
 477          write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
 478          do i=1,ntyp
 479           write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),
 480      &     gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
 481          enddo
 482         endif
 483       else if (tbf) then
 484         if(me.eq.king.or..not.out1file)then
 485          write (iout,'(a)') "Berendsen bath calculation"
 486          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 487          write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
 488          if (reset_moment)
 489      &   write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 490      &   count_reset_moment," steps"
 491          if (reset_vel)
 492      &    write (iout,'(a,i10,a)')
 493      &    "Velocities will be reset at random every",count_reset_vel,
 494      &   " steps"
 495         endif
 496       else if (tnp .or. tnp1 .or. tnh) then
 497         if (tnp .or. tnp1) then
 498            write (iout,'(a)') "Nose-Poincare bath calculation"
 499            if (tnp) write (iout,'(a)')
 500      & "J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird"
 501            if (tnp1) write (iout,'(a)') "JPSJ 70 75 (2001) S. Nose"
 502         else
 503            write (iout,'(a)') "Nose-Hoover bath calculation"
 504            write (iout,'(a)') "Mol.Phys. 87 1117 (1996) Martyna et al."
 505               nresn=1
 506               nyosh=1
 507               nnos=1
 508               do i=1,nnos
 509                qmass(i)=Q_np
 510                xlogs(i)=1.0
 511                vlogs(i)=0.0
 512               enddo
 513               do i=1,nyosh
 514                WDTI(i) = 1.0*d_time/nresn
 515                WDTI2(i)=WDTI(i)/2
 516                WDTI4(i)=WDTI(i)/4
 517                WDTI8(i)=WDTI(i)/8
 518               enddo
 519               if (RESPA) then
 520                if(xiresp) then
 521                  write (iout,'(a)') "NVT-XI-RESPA algorithm"
 522                else
 523                  write (iout,'(a)') "NVT-XO-RESPA algorithm"
 524                endif
 525                do i=1,nyosh
 526                 WDTIi(i) = 1.0*d_time/nresn/ntime_split
 527                 WDTIi2(i)=WDTIi(i)/2
 528                 WDTIi4(i)=WDTIi(i)/4
 529                 WDTIi8(i)=WDTIi(i)/8
 530                enddo
 531               endif
 532         endif
 533
 534         write (iout,'(a60,f10.5)') "Temperature:",t_bath
 535         write (iout,'(a60,f10.5)') "Q =",Q_np
 536         if (reset_moment)
 537      &  write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 538      &   count_reset_moment," steps"
 539         if (reset_vel)
 540      &    write (iout,'(a,i10,a)')
 541      &    "Velocities will be reset at random every",count_reset_vel,
 542      &   " steps"
 543
 544       else if (hmc.gt.0) then
 545          write (iout,'(a)') "Hybrid Monte Carlo calculation"
 546          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 547          write (iout,'(a60,i10)')
 548      &         "Number of MD steps between Metropolis tests:",hmc
 549
 550       else
 551         if(me.eq.king.or..not.out1file)
 552      &   write (iout,'(a31)') "Microcanonical mode calculation"
 553       endif
 554       if(me.eq.king.or..not.out1file)then
 555        if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
 556        if (usampl) then
 557           write(iout,*) "MD running with constraints."
 558           write(iout,*) "Equilibration time ", eq_time, " mtus."
 559           write(iout,*) "Constraining ", nfrag," fragments."
 560           write(iout,*) "Length of each fragment, weight and q0:"
 561           do iset=1,nset
 562            write (iout,*) "Set of restraints #",iset
 563            do i=1,nfrag
 564               write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),
 565      &           ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
 566            enddo
 567            write(iout,*) "constraints between ", npair, "fragments."
 568            write(iout,*) "constraint pairs, weights and q0:"
 569            do i=1,npair
 570             write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),
 571      &             ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
 572            enddo
 573            write(iout,*) "angle constraints within ", nfrag_back,
 574      &      "backbone fragments."
 575            write(iout,*) "fragment, weights:"
 576            do i=1,nfrag_back
 577             write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),
 578      &         ifrag_back(2,i,iset),wfrag_back(1,i,iset),
 579      &         wfrag_back(2,i,iset),wfrag_back(3,i,iset)
 580            enddo
 581           enddo
 582         iset=mod(kolor,nset)+1
 583        endif
 584       endif
 585       if(me.eq.king.or..not.out1file)
 586      & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
 587       return
 588       end
 589 c------------------------------------------------------------------------------
 590       subroutine molread
 591 C
 592 C Read molecular data.
 593 C
 594       implicit real*8 (a-h,o-z)
 595       include 'DIMENSIONS'
 596 #ifdef MPI
 597       include 'mpif.h'
 598       integer error_msg
 599 #endif
 600       include 'COMMON.IOUNITS'
 601       include 'COMMON.GEO'
 602       include 'COMMON.VAR'
 603       include 'COMMON.INTERACT'
 604       include 'COMMON.LOCAL'
 605       include 'COMMON.NAMES'
 606       include 'COMMON.CHAIN'
 607       include 'COMMON.FFIELD'
 608       include 'COMMON.SBRIDGE'
 609       include 'COMMON.HEADER'
 610       include 'COMMON.CONTROL'
 611       include 'COMMON.DBASE'
 612       include 'COMMON.THREAD'
 613       include 'COMMON.CONTACTS'
 614       include 'COMMON.TORCNSTR'
 615       include 'COMMON.TIME1'
 616       include 'COMMON.BOUNDS'
 617       include 'COMMON.MD'
 618       include 'COMMON.REMD'
 619       include 'COMMON.SETUP'
 620       character*4 sequence(maxres)
 621       integer rescode
 622       double precision x(maxvar)
 623       character*256 pdbfile
 624       character*320 weightcard
 625       character*80 weightcard_t,ucase
 626       dimension itype_pdb(maxres)
 627       common /pizda/ itype_pdb
 628       logical seq_comp,fail
 629       double precision energia(0:n_ene)
 630       integer ilen
 631       external ilen
 632 C
 633 C Body
 634 C
 635 C Read weights of the subsequent energy terms.
 636       if(hremd.gt.0) then
 637
 638        k=0
 639        do il=1,hremd
 640         do i=1,nrep
 641          do j=1,remd_m(i)
 642           i2set(k)=il
 643           k=k+1
 644          enddo
 645         enddo
 646        enddo
 647
 648        if(me.eq.king.or..not.out1file) then
 649         write (iout,*) 'Reading ',hremd,' sets of weights for HREMD'
 650         write (iout,*) 'Current weights for processor ',
 651      &                 me,' set ',i2set(me)
 652        endif
 653
 654        do i=1,hremd
 655          call card_concat(weightcard)
 656          call reada(weightcard,'WLONG',wlong,1.0D0)
 657          call reada(weightcard,'WSC',wsc,wlong)
 658          call reada(weightcard,'WSCP',wscp,wlong)
 659          call reada(weightcard,'WELEC',welec,1.0D0)
 660          call reada(weightcard,'WVDWPP',wvdwpp,welec)
 661          call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 662          call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 663          call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 664          call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 665          call reada(weightcard,'WTURN3',wturn3,1.0D0)
 666          call reada(weightcard,'WTURN4',wturn4,1.0D0)
 667          call reada(weightcard,'WTURN6',wturn6,1.0D0)
 668          call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 669          call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 670          call reada(weightcard,'WBOND',wbond,1.0D0)
 671          call reada(weightcard,'WTOR',wtor,1.0D0)
 672          call reada(weightcard,'WTORD',wtor_d,1.0D0)
 673          call reada(weightcard,'WANG',wang,1.0D0)
 674          call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 675          call reada(weightcard,'SCAL14',scal14,0.4D0)
 676          call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 677          call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 678          call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 679          call reada(weightcard,'TEMP0',temp0,300.0d0)
 680          if (index(weightcard,'SOFT').gt.0) ipot=6
 681 C 12/1/95 Added weight for the multi-body term WCORR
 682          call reada(weightcard,'WCORRH',wcorr,1.0D0)
 683          if (wcorr4.gt.0.0d0) wcorr=wcorr4
 684
 685          hweights(i,1)=wsc
 686          hweights(i,2)=wscp
 687          hweights(i,3)=welec
 688          hweights(i,4)=wcorr
 689          hweights(i,5)=wcorr5
 690          hweights(i,6)=wcorr6
 691          hweights(i,7)=wel_loc
 692          hweights(i,8)=wturn3
 693          hweights(i,9)=wturn4
 694          hweights(i,10)=wturn6
 695          hweights(i,11)=wang
 696          hweights(i,12)=wscloc
 697          hweights(i,13)=wtor
 698          hweights(i,14)=wtor_d
 699          hweights(i,15)=wstrain
 700          hweights(i,16)=wvdwpp
 701          hweights(i,17)=wbond
 702          hweights(i,18)=scal14
 703          hweights(i,21)=wsccor
 704
 705        enddo
 706
 707        do i=1,n_ene
 708          weights(i)=hweights(i2set(me),i)
 709        enddo
 710        wsc    =weights(1)
 711        wscp   =weights(2)
 712        welec  =weights(3)
 713        wcorr  =weights(4)
 714        wcorr5 =weights(5)
 715        wcorr6 =weights(6)
 716        wel_loc=weights(7)
 717        wturn3 =weights(8)
 718        wturn4 =weights(9)
 719        wturn6 =weights(10)
 720        wang   =weights(11)
 721        wscloc =weights(12)
 722        wtor   =weights(13)
 723        wtor_d =weights(14)
 724        wstrain=weights(15)
 725        wvdwpp =weights(16)
 726        wbond  =weights(17)
 727        scal14 =weights(18)
 728        wsccor =weights(21)
 729
 730
 731       else
 732        call card_concat(weightcard)
 733        call reada(weightcard,'WLONG',wlong,1.0D0)
 734        call reada(weightcard,'WSC',wsc,wlong)
 735        call reada(weightcard,'WSCP',wscp,wlong)
 736        call reada(weightcard,'WELEC',welec,1.0D0)
 737        call reada(weightcard,'WVDWPP',wvdwpp,welec)
 738        call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 739        call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 740        call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 741        call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 742        call reada(weightcard,'WTURN3',wturn3,1.0D0)
 743        call reada(weightcard,'WTURN4',wturn4,1.0D0)
 744        call reada(weightcard,'WTURN6',wturn6,1.0D0)
 745        call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 746        call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 747        call reada(weightcard,'WBOND',wbond,1.0D0)
 748        call reada(weightcard,'WTOR',wtor,1.0D0)
 749        call reada(weightcard,'WTORD',wtor_d,1.0D0)
 750        call reada(weightcard,'WANG',wang,1.0D0)
 751        call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 752        call reada(weightcard,'SCAL14',scal14,0.4D0)
 753        call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 754        call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 755        call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 756        call reada(weightcard,'TEMP0',temp0,300.0d0)
 757        if (index(weightcard,'SOFT').gt.0) ipot=6
 758 C 12/1/95 Added weight for the multi-body term WCORR
 759        call reada(weightcard,'WCORRH',wcorr,1.0D0)
 760        if (wcorr4.gt.0.0d0) wcorr=wcorr4
 761        weights(1)=wsc
 762        weights(2)=wscp
 763        weights(3)=welec
 764        weights(4)=wcorr
 765        weights(5)=wcorr5
 766        weights(6)=wcorr6
 767        weights(7)=wel_loc
 768        weights(8)=wturn3
 769        weights(9)=wturn4
 770        weights(10)=wturn6
 771        weights(11)=wang
 772        weights(12)=wscloc
 773        weights(13)=wtor
 774        weights(14)=wtor_d
 775        weights(15)=wstrain
 776        weights(16)=wvdwpp
 777        weights(17)=wbond
 778        weights(18)=scal14
 779        weights(21)=wsccor
 780       endif
 781
 782       if(me.eq.king.or..not.out1file)
 783      & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 784      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 785      &  wturn4,wturn6
 786    10 format (/'Energy-term weights (unscaled):'//
 787      & 'WSCC=   ',f10.6,' (SC-SC)'/
 788      & 'WSCP=   ',f10.6,' (SC-p)'/
 789      & 'WELEC=  ',f10.6,' (p-p electr)'/
 790      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 791      & 'WBOND=  ',f10.6,' (stretching)'/
 792      & 'WANG=   ',f10.6,' (bending)'/
 793      & 'WSCLOC= ',f10.6,' (SC local)'/
 794      & 'WTOR=   ',f10.6,' (torsional)'/
 795      & 'WTORD=  ',f10.6,' (double torsional)'/
 796      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 797      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 798      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 799      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 800      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 801      & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
 802      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 803      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 804      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 805       if(me.eq.king.or..not.out1file)then
 806        if (wcorr4.gt.0.0d0) then
 807         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
 808      &   'between contact pairs of peptide groups'
 809         write (iout,'(2(a,f5.3/))')
 810      &  'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
 811      &  'Range of quenching the correlation terms:',2*delt_corr
 812        else if (wcorr.gt.0.0d0) then
 813         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
 814      &   'between contact pairs of peptide groups'
 815        endif
 816        write (iout,'(a,f8.3)')
 817      &  'Scaling factor of 1,4 SC-p interactions:',scal14
 818        write (iout,'(a,f8.3)')
 819      &  'General scaling factor of SC-p interactions:',scalscp
 820       endif
 821       r0_corr=cutoff_corr-delt_corr
 822       do i=1,20
 823         aad(i,1)=scalscp*aad(i,1)
 824         aad(i,2)=scalscp*aad(i,2)
 825         bad(i,1)=scalscp*bad(i,1)
 826         bad(i,2)=scalscp*bad(i,2)
 827       enddo
 828       call rescale_weights(t_bath)
 829       if(me.eq.king.or..not.out1file)
 830      & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 831      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 832      &  wturn4,wturn6
 833    22 format (/'Energy-term weights (scaled):'//
 834      & 'WSCC=   ',f10.6,' (SC-SC)'/
 835      & 'WSCP=   ',f10.6,' (SC-p)'/
 836      & 'WELEC=  ',f10.6,' (p-p electr)'/
 837      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 838      & 'WBOND=  ',f10.6,' (stretching)'/
 839      & 'WANG=   ',f10.6,' (bending)'/
 840      & 'WSCLOC= ',f10.6,' (SC local)'/
 841      & 'WTOR=   ',f10.6,' (torsional)'/
 842      & 'WTORD=  ',f10.6,' (double torsional)'/
 843      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 844      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 845      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 846      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 847      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 848      & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
 849      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 850      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 851      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 852       if(me.eq.king.or..not.out1file)
 853      & write (iout,*) "Reference temperature for weights calculation:",
 854      &  temp0
 855       call reada(weightcard,"D0CM",d0cm,3.78d0)
 856       call reada(weightcard,"AKCM",akcm,15.1d0)
 857       call reada(weightcard,"AKTH",akth,11.0d0)
 858       call reada(weightcard,"AKCT",akct,12.0d0)
 859       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 860       call reada(weightcard,"V2SS",v2ss,7.61d0)
 861       call reada(weightcard,"V3SS",v3ss,13.7d0)
 862       call reada(weightcard,"EBR",ebr,-5.50D0)
 863       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 864       do i=1,maxres
 865         dyn_ss_mask(i)=.false.
 866       enddo
 867       do i=1,maxres-1
 868         do j=i+1,maxres
 869           dyn_ssbond_ij(i,j)=1.0d300
 870         enddo
 871       enddo
 872       call reada(weightcard,"HT",Ht,0.0D0)
 873       if (dyn_ss) then
 874         ss_depth=ebr/wsc-0.25*eps(1,1)
 875         Ht=Ht/wsc-0.25*eps(1,1)
 876         akcm=akcm*wstrain/wsc
 877         akth=akth*wstrain/wsc
 878         akct=akct*wstrain/wsc
 879         v1ss=v1ss*wstrain/wsc
 880         v2ss=v2ss*wstrain/wsc
 881         v3ss=v3ss*wstrain/wsc
 882       else
 883         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 884       endif
 885
 886       if(me.eq.king.or..not.out1file) then
 887        write (iout,*) "Parameters of the SS-bond potential:"
 888        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
 889      & " AKCT",akct
 890        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 891        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 892        write (iout,*)" HT",Ht
 893        print *,'indpdb=',indpdb,' pdbref=',pdbref
 894       endif
 895       if (indpdb.gt.0 .or. pdbref) then
 896         read(inp,'(a)') pdbfile
 897         if(me.eq.king.or..not.out1file)
 898      &   write (iout,'(2a)') 'PDB data will be read from file ',
 899      &   pdbfile(:ilen(pdbfile))
 900         open(ipdbin,file=pdbfile,status='old',err=33)
 901         goto 34
 902   33    write (iout,'(a)') 'Error opening PDB file.'
 903         stop
 904   34    continue
 905 c        print *,'Begin reading pdb data'
 906         call readpdb
 907 c        print *,'Finished reading pdb data'
 908         if(me.eq.king.or..not.out1file)
 909      &   write (iout,'(a,i3,a,i3)')'nsup=',nsup,
 910      &   ' nstart_sup=',nstart_sup
 911         do i=1,nres
 912           itype_pdb(i)=itype(i)
 913         enddo
 914         close (ipdbin)
 915         nnt=nstart_sup
 916         nct=nstart_sup+nsup-1
 917         call contact(.false.,ncont_ref,icont_ref,co)
 918
 919         if (sideadd) then
 920 C Following 2 lines for diagnostics; comment out if not needed
 921          write (iout,*) "Before sideadd"
 922          call intout
 923          if(me.eq.king.or..not.out1file)
 924      &    write(iout,*)'Adding sidechains'
 925          maxsi=1000
 926          do i=2,nres-1
 927           iti=itype(i)
 928           if (iti.ne.10) then
 929             nsi=0
 930             fail=.true.
 931             do while (fail.and.nsi.le.maxsi)
 932               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 933               nsi=nsi+1
 934             enddo
 935             if(fail) write(iout,*)'Adding sidechain failed for res ',
 936      &              i,' after ',nsi,' trials'
 937           endif
 938          enddo
 939 C 10/03/12 Adam: Recalculate coordinates with new side chain positions
 940          call chainbuild
 941         endif
 942 C Following 2 lines for diagnostics; comment out if not needed
 943         write (iout,*) "After sideadd"
 944         call intout
 945       endif
 946       if (indpdb.eq.0) then
 947 C Read sequence if not taken from the pdb file.
 948         read (inp,*) nres
 949 c        print *,'nres=',nres
 950         if (iscode.gt.0) then
 951           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 952         else
 953           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 954         endif
 955 C Convert sequence to numeric code
 956         do i=1,nres
 957           itype(i)=rescode(i,sequence(i),iscode)
 958         enddo
 959 C Assign initial virtual bond lengths
 960         do i=2,nres
 961           vbld(i)=vbl
 962           vbld_inv(i)=vblinv
 963         enddo
 964         do i=2,nres-1
 965           vbld(i+nres)=dsc(itype(i))
 966           vbld_inv(i+nres)=dsc_inv(itype(i))
 967 c          write (iout,*) "i",i," itype",itype(i),
 968 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 969         enddo
 970       endif
 971 c      print *,nres
 972 c      print '(20i4)',(itype(i),i=1,nres)
 973       do i=1,nres
 974 #ifdef PROCOR
 975         if (itype(i).eq.21 .or. itype(i+1).eq.21) then
 976 #else
 977         if (itype(i).eq.21) then
 978 #endif
 979           itel(i)=0
 980 #ifdef PROCOR
 981         else if (itype(i+1).ne.20) then
 982 #else
 983         else if (itype(i).ne.20) then
 984 #endif
 985           itel(i)=1
 986         else
 987           itel(i)=2
 988         endif
 989       enddo
 990       if(me.eq.king.or..not.out1file)then
 991        write (iout,*) "ITEL"
 992        do i=1,nres-1
 993          write (iout,*) i,itype(i),itel(i)
 994        enddo
 995        print *,'Call Read_Bridge.'
 996       endif
 997       call read_bridge
 998 C 8/13/98 Set limits to generating the dihedral angles
 999       do i=1,nres
1000         phibound(1,i)=-pi
1001         phibound(2,i)=pi
1002       enddo
1003       read (inp,*) ndih_constr
1004       if (ndih_constr.gt.0) then
1005         read (inp,*) ftors
1006         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
1007         if(me.eq.king.or..not.out1file)then
1008          write (iout,*)
1009      &   'There are',ndih_constr,' constraints on phi angles.'
1010          do i=1,ndih_constr
1011           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
1012          enddo
1013         endif
1014         do i=1,ndih_constr
1015           phi0(i)=deg2rad*phi0(i)
1016           drange(i)=deg2rad*drange(i)
1017         enddo
1018         if(me.eq.king.or..not.out1file)
1019      &   write (iout,*) 'FTORS',ftors
1020         do i=1,ndih_constr
1021           ii = idih_constr(i)
1022           phibound(1,ii) = phi0(i)-drange(i)
1023           phibound(2,ii) = phi0(i)+drange(i)
1024         enddo
1025       endif
1026       nnt=1
1027 #ifdef MPI
1028       if (me.eq.king) then
1029 #endif
1030        write (iout,'(a)') 'Boundaries in phi angle sampling:'
1031        do i=1,nres
1032          write (iout,'(a3,i5,2f10.1)')
1033      &   restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1034        enddo
1035 #ifdef MP
1036       endif
1037 #endif
1038       nct=nres
1039 cd      print *,'NNT=',NNT,' NCT=',NCT
1040       if (itype(1).eq.21) nnt=2
1041       if (itype(nres).eq.21) nct=nct-1
1042       if (pdbref) then
1043         if(me.eq.king.or..not.out1file)
1044      &   write (iout,'(a,i3)') 'nsup=',nsup
1045         nstart_seq=nnt
1046         if (nsup.le.(nct-nnt+1)) then
1047           do i=0,nct-nnt+1-nsup
1048             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
1049               nstart_seq=nnt+i
1050               goto 111
1051             endif
1052           enddo
1053           write (iout,'(a)')
1054      &            'Error - sequences to be superposed do not match.'
1055           stop
1056         else
1057           do i=0,nsup-(nct-nnt+1)
1058             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
1059      &      then
1060               nstart_sup=nstart_sup+i
1061               nsup=nct-nnt+1
1062               goto 111
1063             endif
1064           enddo
1065           write (iout,'(a)')
1066      &            'Error - sequences to be superposed do not match.'
1067         endif
1068   111   continue
1069         if (nsup.eq.0) nsup=nct-nnt
1070         if (nstart_sup.eq.0) nstart_sup=nnt
1071         if (nstart_seq.eq.0) nstart_seq=nnt
1072         if(me.eq.king.or..not.out1file)
1073      &   write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
1074      &                 ' nstart_seq=',nstart_seq
1075       endif
1076 c--- Zscore rms -------
1077       if (nz_start.eq.0) nz_start=nnt
1078       if (nz_end.eq.0 .and. nsup.gt.0) then
1079         nz_end=nnt+nsup-1
1080       else if (nz_end.eq.0) then
1081         nz_end=nct
1082       endif
1083       if(me.eq.king.or..not.out1file)then
1084        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1085        write (iout,*) 'IZ_SC=',iz_sc
1086       endif
1087 c----------------------
1088       call init_int_table
1089       if (refstr) then
1090         if (.not.pdbref) then
1091           call read_angles(inp,*38)
1092           goto 39
1093    38     write (iout,'(a)') 'Error reading reference structure.'
1094 #ifdef MPI
1095           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1096           stop 'Error reading reference structure'
1097 #endif
1098    39     call chainbuild
1099           call setup_var
1100 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
1101           nstart_sup=nnt
1102           nstart_seq=nnt
1103           nsup=nct-nnt+1
1104           do i=1,2*nres
1105             do j=1,3
1106               cref(j,i)=c(j,i)
1107             enddo
1108           enddo
1109           call contact(.true.,ncont_ref,icont_ref,co)
1110         endif
1111         if(me.eq.king.or..not.out1file)
1112      &   write (iout,*) 'Contact order:',co
1113         if (pdbref) then
1114         if(me.eq.king.or..not.out1file)
1115      &   write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1116         do i=1,ncont_ref
1117           do j=1,2
1118             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1119           enddo
1120           if(me.eq.king.or..not.out1file)
1121      &     write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',
1122      &     icont_ref(1,i),' ',
1123      &     restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
1124         enddo
1125         endif
1126       endif
1127 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1128       if (constr_dist.gt.0) then
1129         call read_dist_constr
1130         call hpb_partition
1131       endif
1132 c      write (iout,*) "After read_dist_constr nhpb",nhpb
1133 c      call flush(iout)
1134       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
1135      &    .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
1136      &    modecalc.ne.10) then
1137 C If input structure hasn't been supplied from the PDB file read or generate
1138 C initial geometry.
1139         if (iranconf.eq.0 .and. .not. extconf) then
1140           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
1141      &     write (iout,'(a)') 'Initial geometry will be read in.'
1142           if (read_cart) then
1143             read(inp,'(8f10.5)',end=36,err=36)
1144      &       ((c(l,k),l=1,3),k=1,nres),
1145      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
1146             call int_from_cart1(.false.)
1147             do i=1,nres-1
1148               do j=1,3
1149                 dc(j,i)=c(j,i+1)-c(j,i)
1150                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1151               enddo
1152             enddo
1153             do i=nnt,nct
1154               if (itype(i).ne.10) then
1155                 do j=1,3
1156                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
1157                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1158                 enddo
1159               endif
1160             enddo
1161             return
1162           else
1163             call read_angles(inp,*36)
1164           endif
1165           goto 37
1166    36     write (iout,'(a)') 'Error reading angle file.'
1167 #ifdef MPI
1168           call mpi_finalize( MPI_COMM_WORLD,IERR )
1169 #endif
1170           stop 'Error reading angle file.'
1171    37     continue
1172         else if (extconf) then
1173          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0)
1174      &    write (iout,'(a)') 'Extended chain initial geometry.'
1175          do i=3,nres
1176           theta(i)=90d0*deg2rad
1177          enddo
1178          do i=4,nres
1179           phi(i)=180d0*deg2rad
1180          enddo
1181          do i=2,nres-1
1182           alph(i)=110d0*deg2rad
1183          enddo
1184          do i=2,nres-1
1185           omeg(i)=-120d0*deg2rad
1186          enddo
1187         else
1188           if(me.eq.king.or..not.out1file)
1189      &     write (iout,'(a)') 'Random-generated initial geometry.'
1190
1191
1192 #ifdef MPI
1193           if (me.eq.king  .or. fg_rank.eq.0 .and. (
1194      &           modecalc.eq.12 .or. modecalc.eq.14) ) then
1195 #endif
1196             do itrial=1,100
1197               itmp=1
1198               call gen_rand_conf(itmp,*30)
1199               goto 40
1200    30         write (iout,*) 'Failed to generate random conformation',
1201      &          ', itrial=',itrial
1202               write (*,*) 'Processor:',me,
1203      &          ' Failed to generate random conformation',
1204      &          ' itrial=',itrial
1205               call intout
1206
1207 #ifdef AIX
1208               call flush_(iout)
1209 #else
1210               call flush(iout)
1211 #endif
1212             enddo
1213             write (iout,'(a,i3,a)') 'Processor:',me,
1214      &        ' error in generating random conformation.'
1215             write (*,'(a,i3,a)') 'Processor:',me,
1216      &        ' error in generating random conformation.'
1217             call flush(iout)
1218 #ifdef MPI
1219             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1220    40       continue
1221           endif
1222 #else
1223    40     continue
1224 #endif
1225         endif
1226       elseif (modecalc.eq.4) then
1227         read (inp,'(a)') intinname
1228         open (intin,file=intinname,status='old',err=333)
1229         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0)
1230      &  write (iout,'(a)') 'intinname',intinname
1231         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1232         goto 334
1233   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1234 #ifdef MPI
1235         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1236 #endif
1237         stop 'Error opening angle file.'
1238   334   continue
1239
1240       endif
1241 C Generate distance constraints, if the PDB structure is to be regularized.
1242       if (nthread.gt.0) then
1243         call read_threadbase
1244       endif
1245       call setup_var
1246       if (me.eq.king .or. .not. out1file)
1247      & call intout
1248       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1249         write (iout,'(/a,i3,a)')
1250      &  'The chain contains',ns,' disulfide-bridging cysteines.'
1251         write (iout,'(20i4)') (iss(i),i=1,ns)
1252        if (dyn_ss) then
1253           write(iout,*)"Running with dynamic disulfide-bond formation"
1254           do i=nss+1,nhpb
1255             ihpb(i-nss)=ihpb(i)
1256             jhpb(i-nss)=jhpb(i)
1257             forcon(i-nss)=forcon(i)
1258             dhpb(i-nss)=dhpb(i)
1259           enddo
1260           nhpb=nhpb-nss
1261           nss=0
1262           call hpb_partition
1263           do i=1,ns
1264             dyn_ss_mask(iss(i))=.true.
1265           enddo
1266        else
1267         write (iout,'(/a/)') 'Pre-formed links are:'
1268         do i=1,nss
1269           i1=ihpb(i)-nres
1270           i2=jhpb(i)-nres
1271           it1=itype(i1)
1272           it2=itype(i2)
1273           if (me.eq.king.or..not.out1file)
1274      &    write (iout,'(2a,i3,3a,i3,a,3f10.3)')
1275      &    restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
1276      &    ebr,forcon(i)
1277         enddo
1278         write (iout,'(a)')
1279        endif
1280       endif
1281       if (i2ndstr.gt.0) call secstrp2dihc
1282 c      call geom_to_var(nvar,x)
1283 c      call etotal(energia(0))
1284 c      call enerprint(energia(0))
1285 c      call briefout(0,etot)
1286 c      stop
1287 cd    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1288 cd    write (iout,'(a)') 'Variable list:'
1289 cd    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1290 #ifdef MPI
1291       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file))
1292      &  write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
1293      &  'Processor',myrank,': end reading molecular data.'
1294 #endif
1295       return
1296       end
1297 c--------------------------------------------------------------------------
1298       logical function seq_comp(itypea,itypeb,length)
1299       implicit none
1300       integer length,itypea(length),itypeb(length)
1301       integer i
1302       do i=1,length
1303         if (itypea(i).ne.itypeb(i)) then
1304           seq_comp=.false.
1305           return
1306         endif
1307       enddo
1308       seq_comp=.true.
1309       return
1310       end
1311 c-----------------------------------------------------------------------------
1312       subroutine read_bridge
1313 C Read information about disulfide bridges.
1314       implicit real*8 (a-h,o-z)
1315       include 'DIMENSIONS'
1316 #ifdef MPI
1317       include 'mpif.h'
1318 #endif
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       include 'COMMON.SETUP'
1334 C Read bridging residues.
1335       read (inp,*) ns,(iss(i),i=1,ns)
1336       print *,'ns=',ns
1337       if(me.eq.king.or..not.out1file)
1338      &  write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
1339 C Check whether the specified bridging residues are cystines.
1340       do i=1,ns
1341         if (itype(iss(i)).ne.1) then
1342           if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
1343      &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
1344      &   ' can form a disulfide bridge?!!!'
1345           write (*,'(2a,i3,a)')
1346      &   'Do you REALLY think that the residue ',restyp(iss(i)),i,
1347      &   ' can form a disulfide bridge?!!!'
1348 #ifdef MPI
1349          call MPI_Finalize(MPI_COMM_WORLD,ierror)
1350          stop
1351 #endif
1352         endif
1353       enddo
1354 C Read preformed bridges.
1355       if (ns.gt.0) then
1356       read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
1357       write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
1358       if (nss.gt.0) then
1359         nhpb=nss
1360 C Check if the residues involved in bridges are in the specified list of
1361 C bridging residues.
1362         do i=1,nss
1363           do j=1,i-1
1364             if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
1365      &      .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
1366               write (iout,'(a,i3,a)') 'Disulfide pair',i,
1367      &      ' contains residues present in other pairs.'
1368               write (*,'(a,i3,a)') 'Disulfide pair',i,
1369      &      ' contains residues present in other pairs.'
1370 #ifdef MPI
1371               call MPI_Finalize(MPI_COMM_WORLD,ierror)
1372               stop
1373 #endif
1374             endif
1375           enddo
1376           do j=1,ns
1377             if (ihpb(i).eq.iss(j)) goto 10
1378           enddo
1379           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1380    10     continue
1381           do j=1,ns
1382             if (jhpb(i).eq.iss(j)) goto 20
1383           enddo
1384           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1385    20     continue
1386           dhpb(i)=dbr
1387           forcon(i)=fbr
1388         enddo
1389         do i=1,nss
1390           ihpb(i)=ihpb(i)+nres
1391           jhpb(i)=jhpb(i)+nres
1392         enddo
1393       endif
1394       endif
1395       return
1396       end
1397 c----------------------------------------------------------------------------
1398       subroutine read_x(kanal,*)
1399       implicit real*8 (a-h,o-z)
1400       include 'DIMENSIONS'
1401       include 'COMMON.GEO'
1402       include 'COMMON.VAR'
1403       include 'COMMON.CHAIN'
1404       include 'COMMON.IOUNITS'
1405       include 'COMMON.CONTROL'
1406       include 'COMMON.LOCAL'
1407       include 'COMMON.INTERACT'
1408 c Read coordinates from input
1409 c
1410       read(kanal,'(8f10.5)',end=10,err=10)
1411      &  ((c(l,k),l=1,3),k=1,nres),
1412      &  ((c(l,k+nres),l=1,3),k=nnt,nct)
1413       do j=1,3
1414         c(j,nres+1)=c(j,1)
1415         c(j,2*nres)=c(j,nres)
1416       enddo
1417       call int_from_cart1(.false.)
1418       do i=1,nres-1
1419         do j=1,3
1420           dc(j,i)=c(j,i+1)-c(j,i)
1421           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
1422         enddo
1423       enddo
1424       do i=nnt,nct
1425         if (itype(i).ne.10) then
1426           do j=1,3
1427             dc(j,i+nres)=c(j,i+nres)-c(j,i)
1428             dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
1429           enddo
1430         endif
1431       enddo
1432
1433       return
1434    10 return1
1435       end
1436 c----------------------------------------------------------------------------
1437       subroutine read_threadbase
1438       implicit real*8 (a-h,o-z)
1439       include 'DIMENSIONS'
1440       include 'COMMON.IOUNITS'
1441       include 'COMMON.GEO'
1442       include 'COMMON.VAR'
1443       include 'COMMON.INTERACT'
1444       include 'COMMON.LOCAL'
1445       include 'COMMON.NAMES'
1446       include 'COMMON.CHAIN'
1447       include 'COMMON.FFIELD'
1448       include 'COMMON.SBRIDGE'
1449       include 'COMMON.HEADER'
1450       include 'COMMON.CONTROL'
1451       include 'COMMON.DBASE'
1452       include 'COMMON.THREAD'
1453       include 'COMMON.TIME1'
1454 C Read pattern database for threading.
1455       read (icbase,*) nseq
1456       do i=1,nseq
1457         read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1458      &   nres_base(2,i),nres_base(3,i)
1459         read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1460      &   nres_base(1,i))
1461 c       write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1462 c    &   nres_base(2,i),nres_base(3,i)
1463 c       write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1464 c    &   nres_base(1,i))
1465       enddo
1466       close (icbase)
1467       if (weidis.eq.0.0D0) weidis=0.1D0
1468       do i=nnt,nct
1469         do j=i+2,nct
1470           nhpb=nhpb+1
1471           ihpb(nhpb)=i
1472           jhpb(nhpb)=j
1473           forcon(nhpb)=weidis
1474         enddo
1475       enddo
1476       read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl)
1477       write (iout,'(a,i5)') 'nexcl: ',nexcl
1478       write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl)
1479       return
1480       end
1481 c------------------------------------------------------------------------------
1482       subroutine setup_var
1483       implicit real*8 (a-h,o-z)
1484       include 'DIMENSIONS'
1485       include 'COMMON.IOUNITS'
1486       include 'COMMON.GEO'
1487       include 'COMMON.VAR'
1488       include 'COMMON.INTERACT'
1489       include 'COMMON.LOCAL'
1490       include 'COMMON.NAMES'
1491       include 'COMMON.CHAIN'
1492       include 'COMMON.FFIELD'
1493       include 'COMMON.SBRIDGE'
1494       include 'COMMON.HEADER'
1495       include 'COMMON.CONTROL'
1496       include 'COMMON.DBASE'
1497       include 'COMMON.THREAD'
1498       include 'COMMON.TIME1'
1499 C Set up variable list.
1500       ntheta=nres-2
1501       nphi=nres-3
1502       nvar=ntheta+nphi
1503       nside=0
1504       do i=2,nres-1
1505         if (itype(i).ne.10) then
1506           nside=nside+1
1507           ialph(i,1)=nvar+nside
1508           ialph(nside,2)=i
1509         endif
1510       enddo
1511       if (indphi.gt.0) then
1512         nvar=nphi
1513       else if (indback.gt.0) then
1514         nvar=nphi+ntheta
1515       else
1516         nvar=nvar+2*nside
1517       endif
1518 cd    write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
1519       return
1520       end
1521 c----------------------------------------------------------------------------
1522       subroutine gen_dist_constr
1523 C Generate CA distance constraints.
1524       implicit real*8 (a-h,o-z)
1525       include 'DIMENSIONS'
1526       include 'COMMON.IOUNITS'
1527       include 'COMMON.GEO'
1528       include 'COMMON.VAR'
1529       include 'COMMON.INTERACT'
1530       include 'COMMON.LOCAL'
1531       include 'COMMON.NAMES'
1532       include 'COMMON.CHAIN'
1533       include 'COMMON.FFIELD'
1534       include 'COMMON.SBRIDGE'
1535       include 'COMMON.HEADER'
1536       include 'COMMON.CONTROL'
1537       include 'COMMON.DBASE'
1538       include 'COMMON.THREAD'
1539       include 'COMMON.TIME1'
1540       dimension itype_pdb(maxres)
1541       common /pizda/ itype_pdb
1542       character*2 iden
1543 cd      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
1544 cd      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
1545 cd     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
1546 cd     & ' nsup',nsup
1547       do i=nstart_sup,nstart_sup+nsup-1
1548 cd      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
1549 cd     &    ' seq_pdb', restyp(itype_pdb(i))
1550         do j=i+2,nstart_sup+nsup-1
1551           nhpb=nhpb+1
1552           ihpb(nhpb)=i+nstart_seq-nstart_sup
1553           jhpb(nhpb)=j+nstart_seq-nstart_sup
1554           forcon(nhpb)=weidis
1555           dhpb(nhpb)=dist(i,j)
1556         enddo
1557       enddo
1558 cd      write (iout,'(a)') 'Distance constraints:'
1559 cd      do i=nss+1,nhpb
1560 cd        ii=ihpb(i)
1561 cd        jj=jhpb(i)
1562 cd        iden='CA'
1563 cd        if (ii.gt.nres) then
1564 cd          iden='SC'
1565 cd          ii=ii-nres
1566 cd          jj=jj-nres
1567 cd        endif
1568 cd        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
1569 cd     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
1570 cd     &  dhpb(i),forcon(i)
1571 cd      enddo
1572       return
1573       end
1574 c----------------------------------------------------------------------------
1575       subroutine map_read
1576       implicit real*8 (a-h,o-z)
1577       include 'DIMENSIONS'
1578       include 'COMMON.MAP'
1579       include 'COMMON.IOUNITS'
1580       character*3 angid(4) /'THE','PHI','ALP','OME'/
1581       character*80 mapcard,ucase
1582       do imap=1,nmap
1583         read (inp,'(a)') mapcard
1584         mapcard=ucase(mapcard)
1585         if (index(mapcard,'PHI').gt.0) then
1586           kang(imap)=1
1587         else if (index(mapcard,'THE').gt.0) then
1588           kang(imap)=2
1589         else if (index(mapcard,'ALP').gt.0) then
1590           kang(imap)=3
1591         else if (index(mapcard,'OME').gt.0) then
1592           kang(imap)=4
1593         else
1594           write(iout,'(a)')'Error - illegal variable spec in MAP card.'
1595           stop 'Error - illegal variable spec in MAP card.'
1596         endif
1597         call readi (mapcard,'RES1',res1(imap),0)
1598         call readi (mapcard,'RES2',res2(imap),0)
1599         if (res1(imap).eq.0) then
1600           res1(imap)=res2(imap)
1601         else if (res2(imap).eq.0) then
1602           res2(imap)=res1(imap)
1603         endif
1604         if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
1605           write (iout,'(a)')
1606      &    'Error - illegal definition of variable group in MAP.'
1607           stop 'Error - illegal definition of variable group in MAP.'
1608         endif
1609         call reada(mapcard,'FROM',ang_from(imap),0.0D0)
1610         call reada(mapcard,'TO',ang_to(imap),0.0D0)
1611         call readi(mapcard,'NSTEP',nstep(imap),0)
1612         if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
1613           write (iout,'(a)')
1614      &     'Illegal boundary and/or step size specification in MAP.'
1615           stop 'Illegal boundary and/or step size specification in MAP.'
1616         endif
1617       enddo ! imap
1618       return
1619       end
1620 c----------------------------------------------------------------------------
1621 csa      subroutine csaread
1622 csa      implicit real*8 (a-h,o-z)
1623 csa      include 'DIMENSIONS'
1624 csa      include 'COMMON.IOUNITS'
1625 csa      include 'COMMON.GEO'
1626 csa      include 'COMMON.CSA'
1627 csa      include 'COMMON.BANK'
1628 csa      include 'COMMON.CONTROL'
1629 csa      character*80 ucase
1630 csa      character*620 mcmcard
1631 csa      call card_concat(mcmcard)
1632 csa
1633 csa      call readi(mcmcard,'NCONF',nconf,50)
1634 csa      call readi(mcmcard,'NADD',nadd,0)
1635 csa      call readi(mcmcard,'JSTART',jstart,1)
1636 csa      call readi(mcmcard,'JEND',jend,1)
1637 csa      call readi(mcmcard,'NSTMAX',nstmax,500000)
1638 csa      call readi(mcmcard,'N0',n0,1)
1639 csa      call readi(mcmcard,'N1',n1,6)
1640 csa      call readi(mcmcard,'N2',n2,4)
1641 csa      call readi(mcmcard,'N3',n3,0)
1642 csa      call readi(mcmcard,'N4',n4,0)
1643 csa      call readi(mcmcard,'N5',n5,0)
1644 csa      call readi(mcmcard,'N6',n6,10)
1645 csa      call readi(mcmcard,'N7',n7,0)
1646 csa      call readi(mcmcard,'N8',n8,0)
1647 csa      call readi(mcmcard,'N9',n9,0)
1648 csa      call readi(mcmcard,'N14',n14,0)
1649 csa      call readi(mcmcard,'N15',n15,0)
1650 csa      call readi(mcmcard,'N16',n16,0)
1651 csa      call readi(mcmcard,'N17',n17,0)
1652 csa      call readi(mcmcard,'N18',n18,0)
1653 csa
1654 csa      vdisulf=(index(mcmcard,'DYNSS').gt.0)
1655 csa
1656 csa      call readi(mcmcard,'NDIFF',ndiff,2)
1657 csa      call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
1658 csa      call readi(mcmcard,'IS1',is1,1)
1659 csa      call readi(mcmcard,'IS2',is2,8)
1660 csa      call readi(mcmcard,'NRAN0',nran0,4)
1661 csa      call readi(mcmcard,'NRAN1',nran1,2)
1662 csa      call readi(mcmcard,'IRR',irr,1)
1663 csa      call readi(mcmcard,'NSEED',nseed,20)
1664 csa      call readi(mcmcard,'NTOTAL',ntotal,10000)
1665 csa      call reada(mcmcard,'CUT1',cut1,2.0d0)
1666 csa      call reada(mcmcard,'CUT2',cut2,5.0d0)
1667 csa      call reada(mcmcard,'ESTOP',estop,-3000.0d0)
1668 csa      call readi(mcmcard,'ICMAX',icmax,3)
1669 csa      call readi(mcmcard,'IRESTART',irestart,0)
1670 csac!bankt      call readi(mcmcard,'NBANKTM',ntbankm,0)
1671 csa      ntbankm=0
1672 csac!bankt
1673 csa      call reada(mcmcard,'DELE',dele,20.0d0)
1674 csa      call reada(mcmcard,'DIFCUT',difcut,720.0d0)
1675 csa      call readi(mcmcard,'IREF',iref,0)
1676 csa      call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
1677 csa      call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
1678 csa      call readi(mcmcard,'NCONF_IN',nconf_in,0)
1679 csa      call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
1680 csa      write (iout,*) "NCONF_IN",nconf_in
1681 csa      return
1682 csa      end
1683 c----------------------------------------------------------------------------
1684 cfmc      subroutine mcmfread
1685 cfmc      implicit real*8 (a-h,o-z)
1686 cfmc      include 'DIMENSIONS'
1687 cfmc      include 'COMMON.MCMF'
1688 cfmc      include 'COMMON.IOUNITS'
1689 cfmc      include 'COMMON.GEO'
1690 cfmc      character*80 ucase
1691 cfmc      character*620 mcmcard
1692 cfmc      call card_concat(mcmcard)
1693 cfmc
1694 cfmc      call readi(mcmcard,'MAXRANT',maxrant,1000)
1695 cfmc      write(iout,*)'MAXRANT=',maxrant
1696 cfmc      call readi(mcmcard,'MAXFAM',maxfam,maxfam_p)
1697 cfmc      write(iout,*)'MAXFAM=',maxfam
1698 cfmc      call readi(mcmcard,'NNET1',nnet1,5)
1699 cfmc      write(iout,*)'NNET1=',nnet1
1700 cfmc      call readi(mcmcard,'NNET2',nnet2,4)
1701 cfmc      write(iout,*)'NNET2=',nnet2
1702 cfmc      call readi(mcmcard,'NNET3',nnet3,4)
1703 cfmc      write(iout,*)'NNET3=',nnet3
1704 cfmc      call readi(mcmcard,'ILASTT',ilastt,0)
1705 cfmc      write(iout,*)'ILASTT=',ilastt
1706 cfmc      call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf)
1707 cfmc      write(iout,*)'MAXSTR=',maxstr
1708 cfmc      maxstr_f=maxstr/maxfam
1709 cfmc      write(iout,*)'MAXSTR_F=',maxstr_f
1710 cfmc      call readi(mcmcard,'NMCMF',nmcmf,10)
1711 cfmc      write(iout,*)'NMCMF=',nmcmf
1712 cfmc      call readi(mcmcard,'IFOCUS',ifocus,nmcmf)
1713 cfmc      write(iout,*)'IFOCUS=',ifocus
1714 cfmc      call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000)
1715 cfmc      write(iout,*)'NLOCMCMF=',nlocmcmf
1716 cfmc      call readi(mcmcard,'INTPRT',intprt,1000)
1717 cfmc      write(iout,*)'INTPRT=',intprt
1718 cfmc      call readi(mcmcard,'IPRT',iprt,100)
1719 cfmc      write(iout,*)'IPRT=',iprt
1720 cfmc      call readi(mcmcard,'IMAXTR',imaxtr,100)
1721 cfmc      write(iout,*)'IMAXTR=',imaxtr
1722 cfmc      call readi(mcmcard,'MAXEVEN',maxeven,1000)
1723 cfmc      write(iout,*)'MAXEVEN=',maxeven
1724 cfmc      call readi(mcmcard,'MAXEVEN1',maxeven1,3)
1725 cfmc      write(iout,*)'MAXEVEN1=',maxeven1
1726 cfmc      call readi(mcmcard,'INIMIN',inimin,200)
1727 cfmc      write(iout,*)'INIMIN=',inimin
1728 cfmc      call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10)
1729 cfmc      write(iout,*)'NSTEPMCMF=',nstepmcmf
1730 cfmc      call readi(mcmcard,'NTHREAD',nthread,5)
1731 cfmc      write(iout,*)'NTHREAD=',nthread
1732 cfmc      call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500)
1733 cfmc      write(iout,*)'MAXSTEPMCMF=',maxstepmcmf
1734 cfmc      call readi(mcmcard,'MAXPERT',maxpert,9)
1735 cfmc      write(iout,*)'MAXPERT=',maxpert
1736 cfmc      call readi(mcmcard,'IRMSD',irmsd,1)
1737 cfmc      write(iout,*)'IRMSD=',irmsd
1738 cfmc      call reada(mcmcard,'DENEMIN',denemin,0.01D0)
1739 cfmc      write(iout,*)'DENEMIN=',denemin
1740 cfmc      call reada(mcmcard,'RCUT1S',rcut1s,3.5D0)
1741 cfmc      write(iout,*)'RCUT1S=',rcut1s
1742 cfmc      call reada(mcmcard,'RCUT1E',rcut1e,2.0D0)
1743 cfmc      write(iout,*)'RCUT1E=',rcut1e
1744 cfmc      call reada(mcmcard,'RCUT2S',rcut2s,0.5D0)
1745 cfmc      write(iout,*)'RCUT2S=',rcut2s
1746 cfmc      call reada(mcmcard,'RCUT2E',rcut2e,0.1D0)
1747 cfmc      write(iout,*)'RCUT2E=',rcut2e
1748 cfmc      call reada(mcmcard,'DPERT1',d_pert1,180.0D0)
1749 cfmc      write(iout,*)'DPERT1=',d_pert1
1750 cfmc      call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0)
1751 cfmc      write(iout,*)'DPERT1A=',d_pert1a
1752 cfmc      call reada(mcmcard,'DPERT2',d_pert2,90.0D0)
1753 cfmc      write(iout,*)'DPERT2=',d_pert2
1754 cfmc      call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0)
1755 cfmc      write(iout,*)'DPERT2A=',d_pert2a
1756 cfmc      call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0)
1757 cfmc      write(iout,*)'DPERT2B=',d_pert2b
1758 cfmc      call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0)
1759 cfmc      write(iout,*)'DPERT2C=',d_pert2c
1760 cfmc      d_pert1=deg2rad*d_pert1
1761 cfmc      d_pert1a=deg2rad*d_pert1a
1762 cfmc      d_pert2=deg2rad*d_pert2
1763 cfmc      d_pert2a=deg2rad*d_pert2a
1764 cfmc      d_pert2b=deg2rad*d_pert2b
1765 cfmc      d_pert2c=deg2rad*d_pert2c
1766 cfmc      call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0)
1767 cfmc      write(iout,*)'KT_MCMF1=',kt_mcmf1
1768 cfmc      call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0)
1769 cfmc      write(iout,*)'KT_MCMF2=',kt_mcmf2
1770 cfmc      call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0)
1771 cfmc      write(iout,*)'DKT_MCMF1=',dkt_mcmf1
1772 cfmc      call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0)
1773 cfmc      write(iout,*)'DKT_MCMF2=',dkt_mcmf2
1774 cfmc      call reada(mcmcard,'RCUTINI',rcutini,3.5D0)
1775 cfmc      write(iout,*)'RCUTINI=',rcutini
1776 cfmc      call reada(mcmcard,'GRAT',grat,0.5D0)
1777 cfmc      write(iout,*)'GRAT=',grat
1778 cfmc      call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0)
1779 cfmc      write(iout,*)'BIAS_MCMF=',bias_mcmf
1780 cfmc
1781 cfmc      return
1782 cfmc      end
1783 c----------------------------------------------------------------------------
1784       subroutine mcmread
1785       implicit real*8 (a-h,o-z)
1786       include 'DIMENSIONS'
1787       include 'COMMON.MCM'
1788       include 'COMMON.MCE'
1789       include 'COMMON.IOUNITS'
1790       character*80 ucase
1791       character*320 mcmcard
1792       call card_concat(mcmcard)
1793       call readi(mcmcard,'MAXACC',maxacc,100)
1794       call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
1795       call readi(mcmcard,'MAXTRIAL',maxtrial,100)
1796       call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
1797       call readi(mcmcard,'MAXREPM',maxrepm,200)
1798       call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
1799       call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
1800       call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
1801       call reada(mcmcard,'E_UP',e_up,5.0D0)
1802       call reada(mcmcard,'DELTE',delte,0.1D0)
1803       call readi(mcmcard,'NSWEEP',nsweep,5)
1804       call readi(mcmcard,'NSTEPH',nsteph,0)
1805       call readi(mcmcard,'NSTEPC',nstepc,0)
1806       call reada(mcmcard,'TMIN',tmin,298.0D0)
1807       call reada(mcmcard,'TMAX',tmax,298.0D0)
1808       call readi(mcmcard,'NWINDOW',nwindow,0)
1809       call readi(mcmcard,'PRINT_MC',print_mc,0)
1810       print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
1811       print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
1812       ent_read=(index(mcmcard,'ENT_READ').gt.0)
1813       call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
1814       call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
1815       call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
1816       call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
1817       call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
1818       if (nwindow.gt.0) then
1819         read (inp,*) (winstart(i),winend(i),i=1,nwindow)
1820         do i=1,nwindow
1821           winlen(i)=winend(i)-winstart(i)+1
1822         enddo
1823       endif
1824       if (tmax.lt.tmin) tmax=tmin
1825       if (tmax.eq.tmin) then
1826         nstepc=0
1827         nsteph=0
1828       endif
1829       if (nstepc.gt.0 .and. nsteph.gt.0) then
1830         tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
1831         tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
1832       endif
1833 C Probabilities of different move types
1834       sumpro_type(0)=0.0D0
1835       call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
1836       call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
1837       sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
1838       call reada(mcmcard,'THETA'     ,sumpro_type(3),0.0d0)
1839       sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
1840       call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
1841       sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
1842       do i=1,MaxMoveType
1843         print *,'i',i,' sumprotype',sumpro_type(i)
1844         sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
1845         print *,'i',i,' sumprotype',sumpro_type(i)
1846       enddo
1847       return
1848       end
1849 c----------------------------------------------------------------------------
1850       subroutine read_minim
1851       implicit real*8 (a-h,o-z)
1852       include 'DIMENSIONS'
1853       include 'COMMON.MINIM'
1854       include 'COMMON.IOUNITS'
1855       character*80 ucase
1856       character*320 minimcard
1857       call card_concat(minimcard)
1858       call readi(minimcard,'MAXMIN',maxmin,2000)
1859       call readi(minimcard,'MAXFUN',maxfun,5000)
1860       call readi(minimcard,'MINMIN',minmin,maxmin)
1861       call readi(minimcard,'MINFUN',minfun,maxmin)
1862       call reada(minimcard,'TOLF',tolf,1.0D-2)
1863       call reada(minimcard,'RTOLF',rtolf,1.0D-4)
1864       print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
1865       print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
1866       print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
1867       write (iout,'(/80(1h*)/20x,a/80(1h*))')
1868      &         'Options in energy minimization:'
1869       write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
1870      & 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
1871      & 'MinMin:',MinMin,' MinFun:',MinFun,
1872      & ' TolF:',TolF,' RTolF:',RTolF
1873       return
1874       end
1875 c----------------------------------------------------------------------------
1876       subroutine read_angles(kanal,*)
1877       implicit real*8 (a-h,o-z)
1878       include 'DIMENSIONS'
1879       include 'COMMON.GEO'
1880       include 'COMMON.VAR'
1881       include 'COMMON.CHAIN'
1882       include 'COMMON.IOUNITS'
1883       include 'COMMON.CONTROL'
1884 c Read angles from input
1885 c
1886        read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
1887        read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
1888        read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
1889        read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
1890
1891        do i=1,nres
1892 c 9/7/01 avoid 180 deg valence angle
1893         if (theta(i).gt.179.99d0) theta(i)=179.99d0
1894 c
1895         theta(i)=deg2rad*theta(i)
1896         phi(i)=deg2rad*phi(i)
1897         alph(i)=deg2rad*alph(i)
1898         omeg(i)=deg2rad*omeg(i)
1899        enddo
1900       return
1901    10 return1
1902       end
1903 c----------------------------------------------------------------------------
1904       subroutine reada(rekord,lancuch,wartosc,default)
1905       implicit none
1906       character*(*) rekord,lancuch
1907       double precision wartosc,default
1908       integer ilen,iread
1909       external ilen
1910       iread=index(rekord,lancuch)
1911       if (iread.eq.0) then
1912         wartosc=default
1913         return
1914       endif
1915       iread=iread+ilen(lancuch)+1
1916       read (rekord(iread:),*,err=10,end=10) wartosc
1917       return
1918   10  wartosc=default
1919       return
1920       end
1921 c----------------------------------------------------------------------------
1922       subroutine readi(rekord,lancuch,wartosc,default)
1923       implicit none
1924       character*(*) rekord,lancuch
1925       integer wartosc,default
1926       integer ilen,iread
1927       external ilen
1928       iread=index(rekord,lancuch)
1929       if (iread.eq.0) then
1930         wartosc=default
1931         return
1932       endif
1933       iread=iread+ilen(lancuch)+1
1934       read (rekord(iread:),*,err=10,end=10) wartosc
1935       return
1936   10  wartosc=default
1937       return
1938       end
1939 c----------------------------------------------------------------------------
1940       subroutine multreadi(rekord,lancuch,tablica,dim,default)
1941       implicit none
1942       integer dim,i
1943       integer tablica(dim),default
1944       character*(*) rekord,lancuch
1945       character*80 aux
1946       integer ilen,iread
1947       external ilen
1948       do i=1,dim
1949         tablica(i)=default
1950       enddo
1951       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1952       if (iread.eq.0) return
1953       iread=iread+ilen(lancuch)+1
1954       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1955    10 return
1956       end
1957 c----------------------------------------------------------------------------
1958       subroutine multreada(rekord,lancuch,tablica,dim,default)
1959       implicit none
1960       integer dim,i
1961       double precision tablica(dim),default
1962       character*(*) rekord,lancuch
1963       character*80 aux
1964       integer ilen,iread
1965       external ilen
1966       do i=1,dim
1967         tablica(i)=default
1968       enddo
1969       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1970       if (iread.eq.0) return
1971       iread=iread+ilen(lancuch)+1
1972       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1973    10 return
1974       end
1975 c----------------------------------------------------------------------------
1976       subroutine openunits
1977       implicit real*8 (a-h,o-z)
1978       include 'DIMENSIONS'
1979 #ifdef MPI
1980       include 'mpif.h'
1981       character*16 form,nodename
1982       integer nodelen
1983 #endif
1984       include 'COMMON.SETUP'
1985       include 'COMMON.IOUNITS'
1986       include 'COMMON.MD'
1987       include 'COMMON.CONTROL'
1988       integer lenpre,lenpot,ilen,lentmp
1989       external ilen
1990       character*3 out1file_text,ucase
1991       character*3 ll
1992       external ucase
1993 c      print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
1994       call getenv_loc("PREFIX",prefix)
1995       pref_orig = prefix
1996       call getenv_loc("POT",pot)
1997       call getenv_loc("DIRTMP",tmpdir)
1998       call getenv_loc("CURDIR",curdir)
1999       call getenv_loc("OUT1FILE",out1file_text)
2000 c      print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
2001       out1file_text=ucase(out1file_text)
2002       if (out1file_text(1:1).eq."Y") then
2003         out1file=.true.
2004       else
2005         out1file=fg_rank.gt.0
2006       endif
2007       lenpre=ilen(prefix)
2008       lenpot=ilen(pot)
2009       lentmp=ilen(tmpdir)
2010       if (lentmp.gt.0) then
2011           write (*,'(80(1h!))')
2012           write (*,'(a,19x,a,19x,a)') "!","  A T T E N T I O N  ","!"
2013           write (*,'(80(1h!))')
2014           write (*,*)"All output files will be on node /tmp directory."
2015 #ifdef MPI
2016         call  MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
2017         if (me.eq.king) then
2018           write (*,*) "The master node is ",nodename
2019         else if (fg_rank.eq.0) then
2020           write (*,*) "I am the CG slave node ",nodename
2021         else
2022           write (*,*) "I am the FG slave node ",nodename
2023         endif
2024 #endif
2025         PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
2026         lenpre = lentmp+lenpre+1
2027       endif
2028       entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
2029 C Get the names and open the input files
2030 #if defined(WINIFL) || defined(WINPGI)
2031       open(1,file=pref_orig(:ilen(pref_orig))//
2032      &  '.inp',status='old',readonly,shared)
2033        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2034 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2035 C Get parameter filenames and open the parameter files.
2036       call getenv_loc('BONDPAR',bondname)
2037       open (ibond,file=bondname,status='old',readonly,shared)
2038       call getenv_loc('THETPAR',thetname)
2039       open (ithep,file=thetname,status='old',readonly,shared)
2040 #ifndef CRYST_THETA
2041       call getenv_loc('THETPARPDB',thetname_pdb)
2042       open (ithep_pdb,file=thetname_pdb,status='old',readonly,shared)
2043 #endif
2044       call getenv_loc('ROTPAR',rotname)
2045       open (irotam,file=rotname,status='old',readonly,shared)
2046 #ifndef CRYST_SC
2047       call getenv_loc('ROTPARPDB',rotname_pdb)
2048       open (irotam_pdb,file=rotname_pdb,status='old',readonly,shared)
2049 #endif
2050       call getenv_loc('TORPAR',torname)
2051       open (itorp,file=torname,status='old',readonly,shared)
2052       call getenv_loc('TORDPAR',tordname)
2053       open (itordp,file=tordname,status='old',readonly,shared)
2054       call getenv_loc('FOURIER',fouriername)
2055       open (ifourier,file=fouriername,status='old',readonly,shared)
2056       call getenv_loc('ELEPAR',elename)
2057       open (ielep,file=elename,status='old',readonly,shared)
2058       call getenv_loc('SIDEPAR',sidename)
2059       open (isidep,file=sidename,status='old',readonly,shared)
2060 #elif (defined CRAY) || (defined AIX)
2061       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
2062      &  action='read')
2063 c      print *,"Processor",myrank," opened file 1"
2064       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2065 c      print *,"Processor",myrank," opened file 9"
2066 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2067 C Get parameter filenames and open the parameter files.
2068       call getenv_loc('BONDPAR',bondname)
2069       open (ibond,file=bondname,status='old',action='read')
2070 c      print *,"Processor",myrank," opened file IBOND"
2071       call getenv_loc('THETPAR',thetname)
2072       open (ithep,file=thetname,status='old',action='read')
2073 c      print *,"Processor",myrank," opened file ITHEP"
2074 #ifndef CRYST_THETA
2075       call getenv_loc('THETPARPDB',thetname_pdb)
2076       open (ithep_pdb,file=thetname_pdb,status='old',action='read')
2077 #endif
2078       call getenv_loc('ROTPAR',rotname)
2079       open (irotam,file=rotname,status='old',action='read')
2080 c      print *,"Processor",myrank," opened file IROTAM"
2081 #ifndef CRYST_SC
2082       call getenv_loc('ROTPARPDB',rotname_pdb)
2083       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
2084 #endif
2085       call getenv_loc('TORPAR',torname)
2086       open (itorp,file=torname,status='old',action='read')
2087 c      print *,"Processor",myrank," opened file ITORP"
2088       call getenv_loc('TORDPAR',tordname)
2089       open (itordp,file=tordname,status='old',action='read')
2090 c      print *,"Processor",myrank," opened file ITORDP"
2091       call getenv_loc('SCCORPAR',sccorname)
2092       open (isccor,file=sccorname,status='old',action='read')
2093 c      print *,"Processor",myrank," opened file ISCCOR"
2094       call getenv_loc('FOURIER',fouriername)
2095       open (ifourier,file=fouriername,status='old',action='read')
2096 c      print *,"Processor",myrank," opened file IFOURIER"
2097       call getenv_loc('ELEPAR',elename)
2098       open (ielep,file=elename,status='old',action='read')
2099 c      print *,"Processor",myrank," opened file IELEP"
2100       call getenv_loc('SIDEPAR',sidename)
2101       open (isidep,file=sidename,status='old',action='read')
2102 c      print *,"Processor",myrank," opened file ISIDEP"
2103 c      print *,"Processor",myrank," opened parameter files"
2104 #elif (defined G77)
2105       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
2106       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2107 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2108 C Get parameter filenames and open the parameter files.
2109       call getenv_loc('BONDPAR',bondname)
2110       open (ibond,file=bondname,status='old')
2111       call getenv_loc('THETPAR',thetname)
2112       open (ithep,file=thetname,status='old')
2113 #ifndef CRYST_THETA
2114       call getenv_loc('THETPARPDB',thetname_pdb)
2115       open (ithep_pdb,file=thetname_pdb,status='old')
2116 #endif
2117       call getenv_loc('ROTPAR',rotname)
2118       open (irotam,file=rotname,status='old')
2119 #ifndef CRYST_SC
2120       call getenv_loc('ROTPARPDB',rotname_pdb)
2121       open (irotam_pdb,file=rotname_pdb,status='old')
2122 #endif
2123       call getenv_loc('TORPAR',torname)
2124       open (itorp,file=torname,status='old')
2125       call getenv_loc('TORDPAR',tordname)
2126       open (itordp,file=tordname,status='old')
2127       call getenv_loc('SCCORPAR',sccorname)
2128       open (isccor,file=sccorname,status='old')
2129       call getenv_loc('FOURIER',fouriername)
2130       open (ifourier,file=fouriername,status='old')
2131       call getenv_loc('ELEPAR',elename)
2132       open (ielep,file=elename,status='old')
2133       call getenv_loc('SIDEPAR',sidename)
2134       open (isidep,file=sidename,status='old')
2135 #else
2136       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
2137      &action='read')
2138        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2139 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2140 C Get parameter filenames and open the parameter files.
2141       call getenv_loc('BONDPAR',bondname)
2142       open (ibond,file=bondname,status='old',action='read')
2143       call getenv_loc('THETPAR',thetname)
2144       open (ithep,file=thetname,status='old',action='read')
2145 #ifndef CRYST_THETA
2146       call getenv_loc('THETPARPDB',thetname_pdb)
2147       print *,"thetname_pdb ",thetname_pdb
2148       open (ithep_pdb,file=thetname_pdb,status='old',action='read')
2149       print *,ithep_pdb," opened"
2150 #endif
2151       call getenv_loc('ROTPAR',rotname)
2152       open (irotam,file=rotname,status='old',action='read')
2153 #ifndef CRYST_SC
2154       call getenv_loc('ROTPARPDB',rotname_pdb)
2155       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
2156 #endif
2157       call getenv_loc('TORPAR',torname)
2158       open (itorp,file=torname,status='old',action='read')
2159       call getenv_loc('TORDPAR',tordname)
2160       open (itordp,file=tordname,status='old',action='read')
2161       call getenv_loc('SCCORPAR',sccorname)
2162       open (isccor,file=sccorname,status='old',action='read')
2163       call getenv_loc('FOURIER',fouriername)
2164       open (ifourier,file=fouriername,status='old',action='read')
2165       call getenv_loc('ELEPAR',elename)
2166       open (ielep,file=elename,status='old',action='read')
2167       call getenv_loc('SIDEPAR',sidename)
2168       open (isidep,file=sidename,status='old',action='read')
2169 #endif
2170 #ifndef OLDSCP
2171 C
2172 C 8/9/01 In the newest version SCp interaction constants are read from a file
2173 C Use -DOLDSCP to use hard-coded constants instead.
2174 C
2175       call getenv_loc('SCPPAR',scpname)
2176 #if defined(WINIFL) || defined(WINPGI)
2177       open (iscpp,file=scpname,status='old',readonly,shared)
2178 #elif (defined CRAY)  || (defined AIX)
2179       open (iscpp,file=scpname,status='old',action='read')
2180 #elif (defined G77)
2181       open (iscpp,file=scpname,status='old')
2182 #else
2183       open (iscpp,file=scpname,status='old',action='read')
2184 #endif
2185 #endif
2186       call getenv_loc('PATTERN',patname)
2187 #if defined(WINIFL) || defined(WINPGI)
2188       open (icbase,file=patname,status='old',readonly,shared)
2189 #elif (defined CRAY)  || (defined AIX)
2190       open (icbase,file=patname,status='old',action='read')
2191 #elif (defined G77)
2192       open (icbase,file=patname,status='old')
2193 #else
2194       open (icbase,file=patname,status='old',action='read')
2195 #endif
2196 #ifdef MPI
2197 C Open output file only for CG processes
2198 c      print *,"Processor",myrank," fg_rank",fg_rank
2199       if (fg_rank.eq.0) then
2200
2201       if (nodes.eq.1) then
2202         npos=3
2203       else
2204         npos = dlog10(dfloat(nodes-1))+1
2205       endif
2206       if (npos.lt.3) npos=3
2207       write (liczba,'(i1)') npos
2208       form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
2209      &  //')'
2210       write (liczba,form) me
2211       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//
2212      &  liczba(:ilen(liczba))
2213       intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2214      &  //'.int'
2215       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2216      &  //'.pdb'
2217       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
2218      &  liczba(:ilen(liczba))//'.mol2'
2219       statname=prefix(:lenpre)//'_'//pot(:lenpot)//
2220      &  liczba(:ilen(liczba))//'.stat'
2221       if (lentmp.gt.0)
2222      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2223      &      //liczba(:ilen(liczba))//'.stat')
2224       rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba))
2225      &  //'.rst'
2226       if(usampl) then
2227           qname=prefix(:lenpre)//'_'//pot(:lenpot)//
2228      & liczba(:ilen(liczba))//'.const'
2229       endif
2230
2231       endif
2232 #else
2233       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
2234       intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
2235       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
2236       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
2237       statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
2238       if (lentmp.gt.0)
2239      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2240      &    //'.stat')
2241       rest2name=prefix(:ilen(prefix))//'.rst'
2242       if(usampl) then
2243          qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
2244       endif
2245 #endif
2246 #if defined(AIX) || defined(PGI)
2247       if (me.eq.king .or. .not. out1file)
2248      &   open(iout,file=outname,status='unknown')
2249 c#define DEBUG
2250 #ifdef DEBUG
2251       if (fg_rank.gt.0) then
2252         write (liczba,'(i3.3)') myrank/nfgtasks
2253         write (ll,'(bz,i3.3)') fg_rank
2254         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2255      &   status='unknown')
2256       endif
2257 #endif
2258 c#undef DEBUG
2259       if(me.eq.king) then
2260        open(igeom,file=intname,status='unknown',position='append')
2261        open(ipdb,file=pdbname,status='unknown')
2262        open(imol2,file=mol2name,status='unknown')
2263        open(istat,file=statname,status='unknown',position='append')
2264       else
2265 c1out       open(iout,file=outname,status='unknown')
2266       endif
2267 #else
2268       if (me.eq.king .or. .not.out1file)
2269      &    open(iout,file=outname,status='unknown')
2270 c#define DEBUG
2271 #ifdef DEBUG
2272       if (fg_rank.gt.0) then
2273         print "Processor",fg_rank," opening output file"
2274         write (liczba,'(i3.3)') myrank/nfgtasks
2275         write (ll,'(bz,i3.3)') fg_rank
2276         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2277      &   status='unknown')
2278       endif
2279 #endif
2280 c#undef DEBUG
2281       if(me.eq.king) then
2282        open(igeom,file=intname,status='unknown',access='append')
2283        open(ipdb,file=pdbname,status='unknown')
2284        open(imol2,file=mol2name,status='unknown')
2285        open(istat,file=statname,status='unknown',access='append')
2286       else
2287 c1out       open(iout,file=outname,status='unknown')
2288       endif
2289 #endif
2290 csa      csa_rbank=prefix(:lenpre)//'.CSA.rbank'
2291 csa      csa_seed=prefix(:lenpre)//'.CSA.seed'
2292 csa      csa_history=prefix(:lenpre)//'.CSA.history'
2293 csa      csa_bank=prefix(:lenpre)//'.CSA.bank'
2294 csa      csa_bank1=prefix(:lenpre)//'.CSA.bank1'
2295 csa      csa_alpha=prefix(:lenpre)//'.CSA.alpha'
2296 csa      csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
2297 csac!bankt      csa_bankt=prefix(:lenpre)//'.CSA.bankt'
2298 csa      csa_int=prefix(:lenpre)//'.int'
2299 csa      csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
2300 csa      csa_native_int=prefix(:lenpre)//'.CSA.native.int'
2301 csa      csa_in=prefix(:lenpre)//'.CSA.in'
2302 c      print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
2303 C Write file names
2304       if (me.eq.king)then
2305       write (iout,'(80(1h-))')
2306       write (iout,'(30x,a)') "FILE ASSIGNMENT"
2307       write (iout,'(80(1h-))')
2308       write (iout,*) "Input file                      : ",
2309      &  pref_orig(:ilen(pref_orig))//'.inp'
2310       write (iout,*) "Output file                     : ",
2311      &  outname(:ilen(outname))
2312       write (iout,*)
2313       write (iout,*) "Sidechain potential file        : ",
2314      &  sidename(:ilen(sidename))
2315 #ifndef OLDSCP
2316       write (iout,*) "SCp potential file              : ",
2317      &  scpname(:ilen(scpname))
2318 #endif
2319       write (iout,*) "Electrostatic potential file    : ",
2320      &  elename(:ilen(elename))
2321       write (iout,*) "Cumulant coefficient file       : ",
2322      &  fouriername(:ilen(fouriername))
2323       write (iout,*) "Torsional parameter file        : ",
2324      &  torname(:ilen(torname))
2325       write (iout,*) "Double torsional parameter file : ",
2326      &  tordname(:ilen(tordname))
2327       write (iout,*) "SCCOR parameter file : ",
2328      &  sccorname(:ilen(sccorname))
2329       write (iout,*) "Bond & inertia constant file    : ",
2330      &  bondname(:ilen(bondname))
2331       write (iout,*) "Bending parameter file          : ",
2332      &  thetname(:ilen(thetname))
2333       write (iout,*) "Rotamer parameter file          : ",
2334      &  rotname(:ilen(rotname))
2335       write (iout,*) "Threading database              : ",
2336      &  patname(:ilen(patname))
2337       if (lentmp.ne.0)
2338      &write (iout,*)" DIRTMP                          : ",
2339      &  tmpdir(:lentmp)
2340       write (iout,'(80(1h-))')
2341       endif
2342       return
2343       end
2344 c----------------------------------------------------------------------------
2345       subroutine card_concat(card)
2346       implicit real*8 (a-h,o-z)
2347       include 'DIMENSIONS'
2348       include 'COMMON.IOUNITS'
2349       character*(*) card
2350       character*80 karta,ucase
2351       external ilen
2352       read (inp,'(a)') karta
2353       karta=ucase(karta)
2354       card=' '
2355       do while (karta(80:80).eq.'&')
2356         card=card(:ilen(card)+1)//karta(:79)
2357         read (inp,'(a)') karta
2358         karta=ucase(karta)
2359       enddo
2360       card=card(:ilen(card)+1)//karta
2361       return
2362       end
2363 c----------------------------------------------------------------------------------
2364       subroutine readrst
2365       implicit real*8 (a-h,o-z)
2366       include 'DIMENSIONS'
2367       include 'COMMON.CHAIN'
2368       include 'COMMON.IOUNITS'
2369       include 'COMMON.MD'
2370       open(irest2,file=rest2name,status='unknown')
2371       read(irest2,*) totT,EK,potE,totE,t_bath
2372       do i=1,2*nres
2373          read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
2374       enddo
2375       do i=1,2*nres
2376          read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
2377       enddo
2378       if(usampl) then
2379              read (irest2,*) iset
2380       endif
2381       close(irest2)
2382       return
2383       end
2384 c---------------------------------------------------------------------------------
2385       subroutine read_fragments
2386       implicit real*8 (a-h,o-z)
2387       include 'DIMENSIONS'
2388 #ifdef MPI
2389       include 'mpif.h'
2390 #endif
2391       include 'COMMON.SETUP'
2392       include 'COMMON.CHAIN'
2393       include 'COMMON.IOUNITS'
2394       include 'COMMON.MD'
2395       include 'COMMON.CONTROL'
2396       read(inp,*) nset,nfrag,npair,nfrag_back
2397       if(me.eq.king.or..not.out1file)
2398      & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
2399      &  " nfrag_back",nfrag_back
2400       do iset=1,nset
2401          read(inp,*) mset(iset)
2402        do i=1,nfrag
2403          read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
2404      &     qinfrag(i,iset)
2405          if(me.eq.king.or..not.out1file)
2406      &    write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
2407      &     ifrag(2,i,iset), qinfrag(i,iset)
2408        enddo
2409        do i=1,npair
2410         read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
2411      &    qinpair(i,iset)
2412         if(me.eq.king.or..not.out1file)
2413      &   write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
2414      &    ipair(2,i,iset), qinpair(i,iset)
2415        enddo
2416        do i=1,nfrag_back
2417         read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2418      &     wfrag_back(3,i,iset),
2419      &     ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2420         if(me.eq.king.or..not.out1file)
2421      &   write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2422      &   wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2423        enddo
2424       enddo
2425       return
2426       end
2427 c-------------------------------------------------------------------------------
2428       subroutine read_dist_constr
2429       implicit real*8 (a-h,o-z)
2430       include 'DIMENSIONS'
2431 #ifdef MPI
2432       include 'mpif.h'
2433 #endif
2434       include 'COMMON.SETUP'
2435       include 'COMMON.CONTROL'
2436       include 'COMMON.CHAIN'
2437       include 'COMMON.IOUNITS'
2438       include 'COMMON.SBRIDGE'
2439       integer ifrag_(2,100),ipair_(2,100)
2440       double precision wfrag_(100),wpair_(100)
2441       character*500 controlcard
2442 c      write (iout,*) "Calling read_dist_constr"
2443 c      write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
2444 c      call flush(iout)
2445       call card_concat(controlcard)
2446       call readi(controlcard,"NFRAG",nfrag_,0)
2447       call readi(controlcard,"NPAIR",npair_,0)
2448       call readi(controlcard,"NDIST",ndist_,0)
2449       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
2450       call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
2451       call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
2452       call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
2453       call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
2454 c      write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
2455 c      write (iout,*) "IFRAG"
2456 c      do i=1,nfrag_
2457 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2458 c      enddo
2459 c      write (iout,*) "IPAIR"
2460 c      do i=1,npair_
2461 c        write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
2462 c      enddo
2463       if (.not.refstr .and. nfrag.gt.0) then
2464         write (iout,*)
2465      &  "ERROR: no reference structure to compute distance restraints"
2466         write (iout,*)
2467      &  "Restraints must be specified explicitly (NDIST=number)"
2468         stop
2469       endif
2470       if (nfrag.lt.2 .and. npair.gt.0) then
2471         write (iout,*) "ERROR: Less than 2 fragments specified",
2472      &   " but distance restraints between pairs requested"
2473         stop
2474       endif
2475       call flush(iout)
2476       do i=1,nfrag_
2477         if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
2478         if (ifrag_(2,i).gt.nstart_sup+nsup-1)
2479      &    ifrag_(2,i)=nstart_sup+nsup-1
2480 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2481         call flush(iout)
2482         if (wfrag_(i).gt.0.0d0) then
2483         do j=ifrag_(1,i),ifrag_(2,i)-1
2484           do k=j+1,ifrag_(2,i)
2485             write (iout,*) "j",j," k",k
2486             ddjk=dist(j,k)
2487             if (constr_dist.eq.1) then
2488             nhpb=nhpb+1
2489             ihpb(nhpb)=j
2490             jhpb(nhpb)=k
2491               dhpb(nhpb)=ddjk
2492             forcon(nhpb)=wfrag_(i)
2493             else if (constr_dist.eq.2) then
2494               if (ddjk.le.dist_cut) then
2495                 nhpb=nhpb+1
2496                 ihpb(nhpb)=j
2497                 jhpb(nhpb)=k
2498                 dhpb(nhpb)=ddjk
2499                 forcon(nhpb)=wfrag_(i)
2500               endif
2501             else
2502               nhpb=nhpb+1
2503               ihpb(nhpb)=j
2504               jhpb(nhpb)=k
2505               dhpb(nhpb)=ddjk
2506               forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
2507             endif
2508 #ifdef MPI
2509             if (.not.out1file .or. me.eq.king)
2510      &      write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2511      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2512 #else
2513             write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2514      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2515 #endif
2516           enddo
2517         enddo
2518         endif
2519       enddo
2520       do i=1,npair_
2521         if (wpair_(i).gt.0.0d0) then
2522         ii = ipair_(1,i)
2523         jj = ipair_(2,i)
2524         if (ii.gt.jj) then
2525           itemp=ii
2526           ii=jj
2527           jj=itemp
2528         endif
2529         do j=ifrag_(1,ii),ifrag_(2,ii)
2530           do k=ifrag_(1,jj),ifrag_(2,jj)
2531             nhpb=nhpb+1
2532             ihpb(nhpb)=j
2533             jhpb(nhpb)=k
2534             forcon(nhpb)=wpair_(i)
2535             dhpb(nhpb)=dist(j,k)
2536 #ifdef MPI
2537             if (.not.out1file .or. me.eq.king)
2538      &      write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2539      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2540 #else
2541             write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2542      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2543 #endif
2544           enddo
2545         enddo
2546         endif
2547       enddo
2548       do i=1,ndist_
2549         read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
2550      &     ibecarb(i),forcon(nhpb+1)
2551         if (forcon(nhpb+1).gt.0.0d0) then
2552           nhpb=nhpb+1
2553           if (ibecarb(i).gt.0) then
2554             ihpb(i)=ihpb(i)+nres
2555             jhpb(i)=jhpb(i)+nres
2556           endif
2557           if (dhpb(nhpb).eq.0.0d0)
2558      &       dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
2559         endif
2560       enddo
2561 #ifdef MPI
2562       if (.not.out1file .or. me.eq.king) then
2563 #endif
2564       do i=1,nhpb
2565           write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
2566      &     i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
2567       enddo
2568       call flush(iout)
2569 #ifdef MPI
2570       endif
2571 #endif
2572       return
2573       end
2574 c-------------------------------------------------------------------------------
2575 #ifdef WINIFL
2576       subroutine flush(iu)
2577       return
2578       end
2579 #endif
2580 #ifdef AIX
2581       subroutine flush(iu)
2582       call flush_(iu)
2583       return
2584       end
2585 #endif
2586 c------------------------------------------------------------------------------
2587       subroutine copy_to_tmp(source)
2588       include "DIMENSIONS"
2589       include "COMMON.IOUNITS"
2590       character*(*) source
2591       character* 256 tmpfile
2592       integer ilen
2593       external ilen
2594       logical ex
2595       tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source))
2596       inquire(file=tmpfile,exist=ex)
2597       if (ex) then
2598         write (*,*) "Copying ",tmpfile(:ilen(tmpfile)),
2599      &   " to temporary directory..."
2600         write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir
2601         call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir)
2602       endif
2603       return
2604       end
2605 c------------------------------------------------------------------------------
2606       subroutine move_from_tmp(source)
2607       include "DIMENSIONS"
2608       include "COMMON.IOUNITS"
2609       character*(*) source
2610       integer ilen
2611       external ilen
2612       write (*,*) "Moving ",source(:ilen(source)),
2613      & " from temporary directory to working directory"
2614       write (*,*) "/bin/mv "//source(:ilen(source))//" "//curdir
2615       call system("/bin/mv "//source(:ilen(source))//" "//curdir)
2616       return
2617       end
2618 c------------------------------------------------------------------------------
2619       subroutine random_init(seed)
2620 C
2621 C Initialize random number generator
2622 C
2623       implicit real*8 (a-h,o-z)
2624       include 'DIMENSIONS'
2625 #ifdef AMD64
2626       integer*8 iseedi8
2627 #endif
2628 #ifdef MPI
2629       include 'mpif.h'
2630       logical OKRandom, prng_restart
2631       real*8  r1
2632       integer iseed_array(4)
2633 #endif
2634       include 'COMMON.IOUNITS'
2635       include 'COMMON.TIME1'
2636       include 'COMMON.THREAD'
2637       include 'COMMON.SBRIDGE'
2638       include 'COMMON.CONTROL'
2639       include 'COMMON.MCM'
2640       include 'COMMON.MAP'
2641       include 'COMMON.HEADER'
2642 csa      include 'COMMON.CSA'
2643       include 'COMMON.CHAIN'
2644       include 'COMMON.MUCA'
2645       include 'COMMON.MD'
2646       include 'COMMON.FFIELD'
2647       include 'COMMON.SETUP'
2648       iseed=-dint(dabs(seed))
2649       if (iseed.eq.0) then
2650         write (iout,'(/80(1h*)/20x,a/80(1h*))')
2651      &    'Random seed undefined. The program will stop.'
2652         write (*,'(/80(1h*)/20x,a/80(1h*))')
2653      &    'Random seed undefined. The program will stop.'
2654 #ifdef MPI
2655         call mpi_finalize(mpi_comm_world,ierr)
2656 #endif
2657         stop 'Bad random seed.'
2658       endif
2659 #ifdef MPI
2660       if (fg_rank.eq.0) then
2661       seed=seed*(me+1)+1
2662 #ifdef AMD64
2663       iseedi8=dint(seed)
2664       if(me.eq.king .or. .not. out1file)
2665      &  write (iout,*) 'MPI: node= ', me, ' iseed= ',iseedi8
2666       write (*,*) 'MPI: node= ', me, ' iseed= ',iseedi8
2667       OKRandom = prng_restart(me,iseedi8)
2668 #else
2669       do i=1,4
2670        tmp=65536.0d0**(4-i)
2671        iseed_array(i) = dint(seed/tmp)
2672        seed=seed-iseed_array(i)*tmp
2673       enddo
2674       if(me.eq.king .or. .not. out1file)
2675      & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ',
2676      &                 (iseed_array(i),i=1,4)
2677       write (*,*) 'MPI: node= ',me, ' iseed(4)= ',
2678      &                 (iseed_array(i),i=1,4)
2679       OKRandom = prng_restart(me,iseed_array)
2680 #endif
2681       if (OKRandom) then
2682         r1=ran_number(0.0D0,1.0D0)
2683         if(me.eq.king .or. .not. out1file)
2684      &   write (iout,*) 'ran_num',r1
2685         if (r1.lt.0.0d0) OKRandom=.false.
2686       endif
2687       if (.not.OKRandom) then
2688         write (iout,*) 'PRNG IS NOT WORKING!!!'
2689         print *,'PRNG IS NOT WORKING!!!'
2690         if (me.eq.0) then
2691          call flush(iout)
2692          call mpi_abort(mpi_comm_world,error_msg,ierr)
2693          stop
2694         else
2695          write (iout,*) 'too many processors for parallel prng'
2696          write (*,*) 'too many processors for parallel prng'
2697          call flush(iout)
2698          stop
2699         endif
2700       endif
2701       endif
2702 #else
2703       call vrndst(iseed)
2704       write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0)
2705 #endif
2706       return
2707       end