source/unres/src_CSA/unres_csa.F

   1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
   2 C                                                                              C
   3 C                                U N R E S                                     C
   4 C                                                                              C
   5 C Program to carry out conformational search of proteins in an united-residue  C
   6 C approximation.                                                               C
   7 C                                                                              C
   8 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
   9       implicit real*8 (a-h,o-z)
  10       include 'DIMENSIONS'
  11
  12
  13 #ifdef MPI
  14       include 'mpif.h'
  15       include 'COMMON.SETUP'
  16 #endif
  17       include 'COMMON.TIME1'
  18       include 'COMMON.INTERACT'
  19       include 'COMMON.NAMES'
  20       include 'COMMON.GEO'
  21       include 'COMMON.HEADER'
  22       include 'COMMON.CONTROL'
  23       include 'COMMON.CONTACTS'
  24       include 'COMMON.CHAIN'
  25       include 'COMMON.VAR'
  26       include 'COMMON.IOUNITS'
  27       include 'COMMON.FFIELD'
  28 c      include 'COMMON.REMD'
  29 c      include 'COMMON.MD'
  30       include 'COMMON.SBRIDGE'
  31       double precision hrtime,mintime,sectime
  32       character*64 text_mode_calc(-2:14) /'test',
  33      & 'SC rotamer distribution',
  34      & 'Energy evaluation or minimization',
  35      & 'Regularization of PDB structure',
  36      & 'Threading of a sequence on PDB structures',
  37      & 'Monte Carlo (with minimization) ',
  38      & 'Energy minimization of multiple conformations',
  39      & 'Checking energy gradient',
  40      & 'Entropic sampling Monte Carlo (with minimization)',
  41      & 'Energy map',
  42      & 'CSA calculations',
  43      & 'Not used 9',
  44      & 'Not used 10',
  45      & 'Soft regularization of PDB structure',
  46      & 'Mesoscopic molecular dynamics (MD) ',
  47      & 'Not used 13',
  48      & 'Replica exchange molecular dynamics (REMD)'/
  49       external ilen
  50
  51 c      call memmon_print_usage()
  52
  53       call init_task
  54       if (me.eq.king)
  55      & write(iout,*)'### LAST MODIFIED  11/03/09 1:19PM by czarek'
  56       if (me.eq.king) call cinfo
  57 C Read force field parameters and job setup data
  58       call readrtns
  59       call flush(iout)
  60 C
  61       if (me.eq.king .or. .not. out1file) then
  62        write (iout,'(2a/)')
  63      & text_mode_calc(modecalc)(:ilen(text_mode_calc(modecalc))),
  64      & ' calculation.'
  65        if (minim) write (iout,'(a)')
  66      &  'Conformations will be energy-minimized.'
  67        write (iout,'(80(1h*)/)')
  68       endif
  69       call flush(iout)
  70 C
  71 c      if (modecalc.eq.-2) then
  72 c        call test
  73 c        stop
  74 c      else if (modecalc.eq.-1) then
  75 c        write(iout,*) "call check_sc_map next"
  76 c        call check_bond
  77 c        stop
  78 c      endif
  79 #ifdef MPI
  80       if (fg_rank.gt.0) then
  81 C Fine-grain slaves just do energy and gradient components.
  82         call ergastulum ! slave workhouse in Latin
  83       else
  84 #endif
  85       if (modecalc.eq.0) then
  86         call exec_eeval_or_minim
  87 c      else if (modecalc.eq.1) then
  88 c        call exec_regularize
  89 c      else if (modecalc.eq.2) then
  90 c        call exec_thread
  91 c      else if (modecalc.eq.3 .or. modecalc .eq.6) then
  92 c        call exec_MC
  93       else if (modecalc.eq.4) then
  94         call exec_mult_eeval_or_minim
  95       else if (modecalc.eq.5) then
  96          call exec_checkgrad
  97 c      else if (ModeCalc.eq.7) then
  98 c        call exec_map
  99       else if (ModeCalc.eq.8) then
 100         call exec_CSA
 101 c      else if (modecalc.eq.11) then
 102 c        call exec_softreg
 103 c      else if (modecalc.eq.12) then
 104 c        call exec_MD
 105 c      else if (modecalc.eq.14) then
 106 c        call exec_MREMD
 107       else
 108         write (iout,'(a)') 'This calculation type is not supported',
 109      &   ModeCalc
 110       endif
 111 #ifdef MPI
 112       endif
 113 C Finish task.
 114       if (fg_rank.eq.0) call finish_task
 115 c      call memmon_print_usage()
 116 #ifdef TIMING
 117        call print_detailed_timing
 118 #endif
 119       call MPI_Finalize(ierr)
 120       stop 'Bye Bye...'
 121 #else
 122       call dajczas(tcpu(),hrtime,mintime,sectime)
 123       stop '********** Program terminated normally.'
 124 #endif
 125       end
 126 c---------------------------------------------------------------------------
 127       subroutine exec_eeval_or_minim
 128       implicit real*8 (a-h,o-z)
 129       include 'DIMENSIONS'
 130 #ifdef MPI
 131       include 'mpif.h'
 132 #endif
 133       include 'COMMON.SETUP'
 134       include 'COMMON.TIME1'
 135       include 'COMMON.INTERACT'
 136       include 'COMMON.NAMES'
 137       include 'COMMON.GEO'
 138       include 'COMMON.HEADER'
 139       include 'COMMON.CONTROL'
 140       include 'COMMON.CONTACTS'
 141       include 'COMMON.CHAIN'
 142       include 'COMMON.VAR'
 143       include 'COMMON.IOUNITS'
 144       include 'COMMON.FFIELD'
 145 c      include 'COMMON.REMD'
 146 c      include 'COMMON.MD'
 147       include 'COMMON.SBRIDGE'
 148       common /srutu/ icall
 149       double precision energy(0:n_ene)
 150       double precision energy_long(0:n_ene),energy_short(0:n_ene)
 151       if (indpdb.eq.0) call chainbuild
 152 c      time00=MPI_Wtime()
 153       call chainbuild_cart
 154 c      if (split_ene) then
 155 c       print *,"Processor",myrank," after chainbuild"
 156 c       icall=1
 157 c       call etotal_long(energy_long(0))
 158 c       write (iout,*) "Printing long range energy"
 159 c       call enerprint(energy_long(0))
 160 c       call etotal_short(energy_short(0))
 161 c       write (iout,*) "Printing short range energy"
 162 c       call enerprint(energy_short(0))
 163 c       do i=0,n_ene
 164 c         energy(i)=energy_long(i)+energy_short(i)
 165 c         write (iout,*) i,energy_long(i),energy_short(i),energy(i)
 166 c       enddo
 167 c       write (iout,*) "Printing long+short range energy"
 168 c       call enerprint(energy(0))
 169 c      endif
 170       call etotal(energy(0))
 171 c      time_ene=MPI_Wtime()-time00
 172       write (iout,*) "Time for energy evaluation",time_ene
 173       print *,"after etotal"
 174       etota = energy(0)
 175       etot =etota
 176       call enerprint(energy(0))
 177 c      call hairpin(.true.,nharp,iharp)
 178 c      call secondary2(.true.)
 179       if (minim) then
 180
 181         if (dccart) then
 182           print *, 'Calling MINIM_DC'
 183 c          time1=MPI_WTIME()
 184           call minim_dc(etot,iretcode,nfun)
 185         else
 186           if (indpdb.ne.0) then
 187             call bond_regular
 188             call chainbuild
 189           endif
 190           call geom_to_var(nvar,varia)
 191           print *,'Calling MINIMIZE.'
 192 c          time1=MPI_WTIME()
 193           call minimize(etot,varia,iretcode,nfun)
 194         endif
 195         print *,'SUMSL return code is',iretcode,' eval ',nfun
 196 c        evals=nfun/(MPI_WTIME()-time1)
 197         print *,'# eval/s',evals
 198         print *,'refstr=',refstr
 199 c        call hairpin(.true.,nharp,iharp)
 200 c        call secondary2(.true.)
 201         call etotal(energy(0))
 202         etot = energy(0)
 203         call enerprint(energy(0))
 204
 205         call intout
 206         call briefout(0,etot)
 207         if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 208           write (iout,'(a,i3)') 'SUMSL return code:',iretcode
 209           write (iout,'(a,i20)') '# of energy evaluations:',nfun+1
 210           write (iout,'(a,f16.3)')'# of energy evaluations/sec:',evals
 211       else
 212         print *,'refstr=',refstr
 213         if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 214         call briefout(0,etot)
 215       endif
 216       if (outpdb) call pdbout(etot,titel(:32),ipdb)
 217       if (outmol2) call mol2out(etot,titel(:32))
 218       return
 219       end
 220
 221       subroutine exec_checkgrad
 222       implicit real*8 (a-h,o-z)
 223       include 'DIMENSIONS'
 224 #ifdef MPI
 225       include 'mpif.h'
 226 #endif
 227       include 'COMMON.SETUP'
 228       include 'COMMON.TIME1'
 229       include 'COMMON.INTERACT'
 230       include 'COMMON.NAMES'
 231       include 'COMMON.GEO'
 232       include 'COMMON.HEADER'
 233       include 'COMMON.CONTROL'
 234       include 'COMMON.CONTACTS'
 235       include 'COMMON.CHAIN'
 236       include 'COMMON.VAR'
 237       include 'COMMON.IOUNITS'
 238       include 'COMMON.FFIELD'
 239 c      include 'COMMON.REMD'
 240       include 'COMMON.MD_'
 241       include 'COMMON.SBRIDGE'
 242       common /srutu/ icall
 243       double precision energy(0:max_ene)
 244 c      do i=2,nres
 245 c        vbld(i)=vbld(i)+ran_number(-0.1d0,0.1d0)
 246 c        if (itype(i).ne.10)
 247 c     &      vbld(i+nres)=vbld(i+nres)+ran_number(-0.001d0,0.001d0)
 248 c      enddo
 249       if (indpdb.eq.0) call chainbuild
 250 c      do i=0,nres
 251 c        do j=1,3
 252 c          dc(j,i)=dc(j,i)+ran_number(-0.2d0,0.2d0)
 253 c        enddo
 254 c      enddo
 255 c      do i=1,nres-1
 256 c        if (itype(i).ne.10) then
 257 c          do j=1,3
 258 c            dc(j,i+nres)=dc(j,i+nres)+ran_number(-0.2d0,0.2d0)
 259 c          enddo
 260 c        endif
 261 c      enddo
 262 c      do j=1,3
 263 c        dc(j,0)=ran_number(-0.2d0,0.2d0)
 264 c      enddo
 265       usampl=.true.
 266       totT=1.d0
 267       eq_time=0.0d0
 268 c      call read_fragments
 269       read(inp,*) t_bath
 270       call rescale_weights(t_bath)
 271       call chainbuild_cart
 272       call cartprint
 273       call intout
 274       icall=1
 275       call etotal(energy(0))
 276       etot = energy(0)
 277       call enerprint(energy(0))
 278       write (iout,*) "Uconst",Uconst," Uconst_back",uconst_back
 279       print *,'icheckgrad=',icheckgrad
 280       goto (10,20,30) icheckgrad
 281   10  call check_ecartint
 282       return
 283   20  call check_cartgrad
 284       return
 285   30  call check_eint
 286       return
 287       end
 288 c---------------------------------------------------------------------------
 289       subroutine exec_CSA
 290 #ifdef MPI
 291       include "mpif.h"
 292 #endif
 293       include 'DIMENSIONS'
 294       include 'COMMON.IOUNITS'
 295 C Conformational Space Annealling programmed by Jooyoung Lee.
 296 C This method works only with parallel machines!
 297 #ifdef MPI
 298       call together
 299 #else
 300       write (iout,*) "CSA works on parallel machines only"
 301 #endif
 302       return
 303       end
 304 c---------------------------------------------------------------------------
 305       subroutine exec_mult_eeval_or_minim
 306       implicit real*8 (a-h,o-z)
 307       include 'DIMENSIONS'
 308       include 'mpif.h'
 309       integer muster(mpi_status_size)
 310       include 'COMMON.SETUP'
 311       include 'COMMON.TIME1'
 312       include 'COMMON.INTERACT'
 313       include 'COMMON.NAMES'
 314       include 'COMMON.GEO'
 315       include 'COMMON.HEADER'
 316       include 'COMMON.CONTROL'
 317       include 'COMMON.CONTACTS'
 318       include 'COMMON.CHAIN'
 319       include 'COMMON.VAR'
 320       include 'COMMON.IOUNITS'
 321       include 'COMMON.FFIELD'
 322       include 'COMMON.SBRIDGE'
 323       double precision varia(maxvar)
 324       integer ind(6)
 325       double precision energy(0:n_ene)
 326       logical eof
 327       eof=.false.
 328
 329       if(me.ne.king) then
 330         call minim_mcmf
 331         return
 332       endif
 333
 334       close (intin)
 335       open(intin,file=intinname,status='old')
 336       write (istat,'(a5,100a12)')"#    ",
 337      &  (wname(print_order(i)),i=1,nprint_ene)
 338       if (refstr) then
 339         write (istat,'(a5,100a12)')"#    ",
 340      &   (ename(print_order(i)),i=1,nprint_ene),
 341      &   "ETOT total","RMSD","nat.contact","nnt.contact",
 342      &   "cont.order","TMscore"
 343       else
 344         write (istat,'(a5,100a12)')"#    ",
 345      &    (ename(print_order(i)),i=1,nprint_ene),"ETOT total"
 346       endif
 347
 348       if (.not.minim) then
 349         do while (.not. eof)
 350           if (read_cart) then
 351             read (intin,'(e15.10,e15.5)',end=1100,err=1100) time,ene
 352             call read_x(intin,*11)
 353 c Broadcast the order to compute internal coordinates to the slaves.
 354             if (nfgtasks.gt.1)
 355      &        call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
 356             call int_from_cart1(.false.)
 357           else
 358             read (intin,'(i5)',end=1100,err=1100) iconf
 359             call read_angles(intin,*11)
 360             call geom_to_var(nvar,varia)
 361             call chainbuild
 362           endif
 363           write (iout,'(a,i7)') 'Conformation #',iconf
 364           call etotal(energy(0))
 365           call briefout(iconf,energy(0))
 366           call enerprint(energy(0))
 367           etot=energy(0)
 368           if (refstr) then
 369             call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 370             call calc_tmscore(tm,.true.)
 371             write (istat,'(i5,100(f12.3))') iconf,
 372      &      (energy(print_order(i)),i=1,nprint_ene),etot,
 373      &       rms,frac,frac_nn,co,tm
 374           else
 375             write (istat,'(i5,100(f12.3))') iconf,
 376      &     (energy(print_order(i)),i=1,nprint_ene),etot
 377           endif
 378         enddo
 379 1100    continue
 380         goto 1101
 381       endif
 382
 383       mm=0
 384       imm=0
 385       nft=0
 386       ene0=0.0d0
 387       n=0
 388       iconf=0
 389       do while (.not. eof)
 390         mm=mm+1
 391         if (mm.lt.nodes) then
 392           if (read_cart) then
 393             read (intin,'(e15.10,e15.5)',end=11,err=11) time,ene
 394             call read_x(intin,*11)
 395 c Broadcast the order to compute internal coordinates to the slaves.
 396             if (nfgtasks.gt.1)
 397      &        call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
 398             call int_from_cart1(.false.)
 399           else
 400             read (intin,'(i5)',end=11,err=11) iconf
 401             call read_angles(intin,*11)
 402             call geom_to_var(nvar,varia)
 403             call chainbuild
 404           endif
 405
 406           n=n+1
 407           write (iout,*) 'Conformation #',iconf,' read'
 408          imm=imm+1
 409          ind(1)=1
 410          ind(2)=n
 411          ind(3)=0
 412          ind(4)=0
 413          ind(5)=0
 414          ind(6)=0
 415          ene0=0.0d0
 416          call mpi_send(ind,6,mpi_integer,mm,idint,CG_COMM,
 417      *                  ierr)
 418          call mpi_send(varia,nvar,mpi_double_precision,mm,
 419      *                  idreal,CG_COMM,ierr)
 420          call mpi_send(ene0,1,mpi_double_precision,mm,
 421      *                  idreal,CG_COMM,ierr)
 422 c         print *,'task ',n,' sent to worker ',mm,nvar
 423         else
 424          call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint,
 425      *                 CG_COMM,muster,ierr)
 426          man=muster(mpi_source)
 427 c         print *,'receiving result from worker ',man,' (',iii1,iii,')'
 428          call mpi_recv(varia,nvar,mpi_double_precision,
 429      *               man,idreal,CG_COMM,muster,ierr)
 430          call mpi_recv(ene,1,
 431      *               mpi_double_precision,man,idreal,
 432      *               CG_COMM,muster,ierr)
 433          call mpi_recv(ene0,1,
 434      *               mpi_double_precision,man,idreal,
 435      *               CG_COMM,muster,ierr)
 436 c         print *,'result received from worker ',man,' sending now'
 437
 438           call var_to_geom(nvar,varia)
 439           call chainbuild
 440           call etotal(energy(0))
 441           iconf=ind(2)
 442           write (iout,*)
 443           write (iout,*)
 444           write (iout,*) 'Conformation #',iconf,ind(5)
 445
 446           etot=energy(0)
 447           call enerprint(energy(0))
 448           call briefout(iconf,etot)
 449           if (refstr) then
 450             call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 451             call calc_tmscore(tm,.true.)
 452             write (istat,'(i5,100(f12.3))') iconf,
 453      &     (energy(print_order(i)),i=1,nprint_ene),etot,
 454      &     rms,frac,frac_nn,co,tm
 455           else
 456             write (istat,'(i5,100(f12.3))') iconf,
 457      &     (energy(print_order(i)),i=1,nprint_ene),etot
 458           endif
 459
 460           imm=imm-1
 461           if (read_cart) then
 462             read (intin,'(e15.10,e15.5)',end=1101,err=1101) time,ene
 463             call read_x(intin,*11)
 464 c Broadcast the order to compute internal coordinates to the slaves.
 465             if (nfgtasks.gt.1)
 466      &        call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
 467             call int_from_cart1(.false.)
 468           else
 469             read (intin,'(i5)',end=1101,err=1101) iconf
 470             call read_angles(intin,*11)
 471             call geom_to_var(nvar,varia)
 472             call chainbuild
 473           endif
 474           n=n+1
 475           write (iout,*) 'Conformation #',iconf,' read'
 476           imm=imm+1
 477           ind(1)=1
 478           ind(2)=n
 479           ind(3)=0
 480           ind(4)=0
 481           ind(5)=0
 482           ind(6)=0
 483           call mpi_send(ind,6,mpi_integer,man,idint,CG_COMM,
 484      *                  ierr)
 485           call mpi_send(varia,nvar,mpi_double_precision,man,
 486      *                  idreal,CG_COMM,ierr)
 487           call mpi_send(ene0,1,mpi_double_precision,man,
 488      *                  idreal,CG_COMM,ierr)
 489           nf_mcmf=nf_mcmf+ind(4)
 490           nmin=nmin+1
 491         endif
 492       enddo
 493 11    continue
 494       do j=1,imm
 495         call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint,
 496      *               CG_COMM,muster,ierr)
 497         man=muster(mpi_source)
 498         call mpi_recv(varia,nvar,mpi_double_precision,
 499      *               man,idreal,CG_COMM,muster,ierr)
 500         call mpi_recv(ene,1,
 501      *               mpi_double_precision,man,idreal,
 502      *               CG_COMM,muster,ierr)
 503         call mpi_recv(ene0,1,
 504      *               mpi_double_precision,man,idreal,
 505      *               CG_COMM,muster,ierr)
 506
 507         call var_to_geom(nvar,varia)
 508         call chainbuild
 509         call etotal(energy(0))
 510         iconf=ind(2)
 511         write (iout,*)
 512         write (iout,*)
 513         write (iout,*) 'Conformation #',iconf,ind(5)
 514
 515         etot=energy(0)
 516         call enerprint(energy(0))
 517         call briefout(iconf,etot)
 518         if (refstr) then
 519           call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
 520           call calc_tmscore(tm,.true.)
 521           write (istat,'(i5,100(f12.3))') iconf,
 522      &   (energy(print_order(i)),i=1,nprint_ene),etot,
 523      &   rms,frac,frac_nn,co,tm
 524         else
 525           write (istat,'(i5,100(f12.3))') iconf,
 526      &    (energy(print_order(i)),i=1,nprint_ene),etot
 527         endif
 528         nmin=nmin+1
 529       enddo
 530 1101  continue
 531       do i=1, nodes-1
 532          ind(1)=0
 533          ind(2)=0
 534          ind(3)=0
 535          ind(4)=0
 536          ind(5)=0
 537          ind(6)=0
 538          call mpi_send(ind,6,mpi_integer,i,idint,CG_COMM,
 539      *                  ierr)
 540       enddo
 541       return
 542       end
 543 c---------------------------------------------------------------------------
 544