CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC C C C U N R E S C C C C Program to carry out conformational search of proteins in an united-residue C C approximation. C C C CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC implicit real*8 (a-h,o-z) include 'DIMENSIONS' #ifdef MPI include 'mpif.h' include 'COMMON.SETUP' #endif include 'COMMON.TIME1' include 'COMMON.INTERACT' include 'COMMON.NAMES' include 'COMMON.GEO' include 'COMMON.HEADER' include 'COMMON.CONTROL' include 'COMMON.CONTACTS' include 'COMMON.CHAIN' include 'COMMON.VAR' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' c include 'COMMON.REMD' c include 'COMMON.MD' include 'COMMON.SBRIDGE' double precision hrtime,mintime,sectime character*64 text_mode_calc(-2:14) /'test', & 'SC rotamer distribution', & 'Energy evaluation or minimization', & 'Regularization of PDB structure', & 'Threading of a sequence on PDB structures', & 'Monte Carlo (with minimization) ', & 'Energy minimization of multiple conformations', & 'Checking energy gradient', & 'Entropic sampling Monte Carlo (with minimization)', & 'Energy map', & 'CSA calculations', & 'Not used 9', & 'Not used 10', & 'Soft regularization of PDB structure', & 'Mesoscopic molecular dynamics (MD) ', & 'Not used 13', & 'Replica exchange molecular dynamics (REMD)'/ external ilen c call memmon_print_usage() call init_task if (me.eq.king) & write(iout,*)'### LAST MODIFIED 11/03/09 1:19PM by czarek' if (me.eq.king) call cinfo C Read force field parameters and job setup data call readrtns call flush(iout) C if (me.eq.king .or. .not. out1file) then write (iout,'(2a/)') & text_mode_calc(modecalc)(:ilen(text_mode_calc(modecalc))), & ' calculation.' if (minim) write (iout,'(a)') & 'Conformations will be energy-minimized.' write (iout,'(80(1h*)/)') endif call flush(iout) C c if (modecalc.eq.-2) then c call test c stop c else if (modecalc.eq.-1) then c write(iout,*) "call check_sc_map next" c call check_bond c stop c endif #ifdef MPI if (fg_rank.gt.0) then C Fine-grain slaves just do energy and gradient components. call ergastulum ! slave workhouse in Latin else #endif if (modecalc.eq.0) then call exec_eeval_or_minim c else if (modecalc.eq.1) then c call exec_regularize c else if (modecalc.eq.2) then c call exec_thread c else if (modecalc.eq.3 .or. modecalc .eq.6) then c call exec_MC else if (modecalc.eq.4) then call exec_mult_eeval_or_minim else if (modecalc.eq.5) then call exec_checkgrad c else if (ModeCalc.eq.7) then c call exec_map else if (ModeCalc.eq.8) then call exec_CSA c else if (modecalc.eq.11) then c call exec_softreg c else if (modecalc.eq.12) then c call exec_MD c else if (modecalc.eq.14) then c call exec_MREMD else write (iout,'(a)') 'This calculation type is not supported', & ModeCalc endif #ifdef MPI endif C Finish task. if (fg_rank.eq.0) call finish_task c call memmon_print_usage() #ifdef TIMING call print_detailed_timing #endif call MPI_Finalize(ierr) stop 'Bye Bye...' #else call dajczas(tcpu(),hrtime,mintime,sectime) stop '********** Program terminated normally.' #endif end c--------------------------------------------------------------------------- subroutine exec_eeval_or_minim implicit real*8 (a-h,o-z) include 'DIMENSIONS' #ifdef MPI include 'mpif.h' #endif include 'COMMON.SETUP' include 'COMMON.TIME1' include 'COMMON.INTERACT' include 'COMMON.NAMES' include 'COMMON.GEO' include 'COMMON.HEADER' include 'COMMON.CONTROL' include 'COMMON.CONTACTS' include 'COMMON.CHAIN' include 'COMMON.VAR' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' c include 'COMMON.REMD' c include 'COMMON.MD' include 'COMMON.SBRIDGE' common /srutu/ icall double precision energy(0:n_ene) double precision energy_long(0:n_ene),energy_short(0:n_ene) if (indpdb.eq.0) call chainbuild c time00=MPI_Wtime() call chainbuild_cart c if (split_ene) then c print *,"Processor",myrank," after chainbuild" c icall=1 c call etotal_long(energy_long(0)) c write (iout,*) "Printing long range energy" c call enerprint(energy_long(0)) c call etotal_short(energy_short(0)) c write (iout,*) "Printing short range energy" c call enerprint(energy_short(0)) c do i=0,n_ene c energy(i)=energy_long(i)+energy_short(i) c write (iout,*) i,energy_long(i),energy_short(i),energy(i) c enddo c write (iout,*) "Printing long+short range energy" c call enerprint(energy(0)) c endif call etotal(energy(0)) c time_ene=MPI_Wtime()-time00 write (iout,*) "Time for energy evaluation",time_ene print *,"after etotal" etota = energy(0) etot =etota call enerprint(energy(0)) c call hairpin(.true.,nharp,iharp) c call secondary2(.true.) if (minim) then if (dccart) then print *, 'Calling MINIM_DC' c time1=MPI_WTIME() call minim_dc(etot,iretcode,nfun) else if (indpdb.ne.0) then call bond_regular call chainbuild endif call geom_to_var(nvar,varia) print *,'Calling MINIMIZE.' c time1=MPI_WTIME() call minimize(etot,varia,iretcode,nfun) endif print *,'SUMSL return code is',iretcode,' eval ',nfun c evals=nfun/(MPI_WTIME()-time1) print *,'# eval/s',evals print *,'refstr=',refstr c call hairpin(.true.,nharp,iharp) c call secondary2(.true.) call etotal(energy(0)) etot = energy(0) call enerprint(energy(0)) call intout call briefout(0,etot) if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.) write (iout,'(a,i3)') 'SUMSL return code:',iretcode write (iout,'(a,i20)') '# of energy evaluations:',nfun+1 write (iout,'(a,f16.3)')'# of energy evaluations/sec:',evals else print *,'refstr=',refstr if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.) call briefout(0,etot) endif if (outpdb) call pdbout(etot,titel(:32),ipdb) if (outmol2) call mol2out(etot,titel(:32)) return end subroutine exec_checkgrad implicit real*8 (a-h,o-z) include 'DIMENSIONS' #ifdef MPI include 'mpif.h' #endif include 'COMMON.SETUP' include 'COMMON.TIME1' include 'COMMON.INTERACT' include 'COMMON.NAMES' include 'COMMON.GEO' include 'COMMON.HEADER' include 'COMMON.CONTROL' include 'COMMON.CONTACTS' include 'COMMON.CHAIN' include 'COMMON.VAR' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' c include 'COMMON.REMD' include 'COMMON.MD_' include 'COMMON.SBRIDGE' common /srutu/ icall double precision energy(0:max_ene) c do i=2,nres c vbld(i)=vbld(i)+ran_number(-0.1d0,0.1d0) c if (itype(i).ne.10) c & vbld(i+nres)=vbld(i+nres)+ran_number(-0.001d0,0.001d0) c enddo if (indpdb.eq.0) call chainbuild c do i=0,nres c do j=1,3 c dc(j,i)=dc(j,i)+ran_number(-0.2d0,0.2d0) c enddo c enddo c do i=1,nres-1 c if (itype(i).ne.10) then c do j=1,3 c dc(j,i+nres)=dc(j,i+nres)+ran_number(-0.2d0,0.2d0) c enddo c endif c enddo c do j=1,3 c dc(j,0)=ran_number(-0.2d0,0.2d0) c enddo usampl=.true. totT=1.d0 eq_time=0.0d0 c call read_fragments read(inp,*) t_bath call rescale_weights(t_bath) call chainbuild_cart call cartprint call intout icall=1 call etotal(energy(0)) etot = energy(0) call enerprint(energy(0)) write (iout,*) "Uconst",Uconst," Uconst_back",uconst_back print *,'icheckgrad=',icheckgrad goto (10,20,30) icheckgrad 10 call check_ecartint return 20 call check_cartgrad return 30 call check_eint return end c--------------------------------------------------------------------------- subroutine exec_CSA #ifdef MPI include "mpif.h" #endif include 'DIMENSIONS' include 'COMMON.IOUNITS' C Conformational Space Annealling programmed by Jooyoung Lee. C This method works only with parallel machines! #ifdef MPI call together #else write (iout,*) "CSA works on parallel machines only" #endif return end c--------------------------------------------------------------------------- subroutine exec_mult_eeval_or_minim implicit real*8 (a-h,o-z) include 'DIMENSIONS' include 'mpif.h' integer muster(mpi_status_size) include 'COMMON.SETUP' include 'COMMON.TIME1' include 'COMMON.INTERACT' include 'COMMON.NAMES' include 'COMMON.GEO' include 'COMMON.HEADER' include 'COMMON.CONTROL' include 'COMMON.CONTACTS' include 'COMMON.CHAIN' include 'COMMON.VAR' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' include 'COMMON.SBRIDGE' double precision varia(maxvar) integer ind(6) double precision energy(0:n_ene) logical eof eof=.false. if(me.ne.king) then call minim_mcmf return endif close (intin) open(intin,file=intinname,status='old') write (istat,'(a5,100a12)')"# ", & (wname(print_order(i)),i=1,nprint_ene) if (refstr) then write (istat,'(a5,100a12)')"# ", & (ename(print_order(i)),i=1,nprint_ene), & "ETOT total","RMSD","nat.contact","nnt.contact", & "cont.order","TMscore" else write (istat,'(a5,100a12)')"# ", & (ename(print_order(i)),i=1,nprint_ene),"ETOT total" endif if (.not.minim) then do while (.not. eof) if (read_cart) then read (intin,'(e15.10,e15.5)',end=1100,err=1100) time,ene call read_x(intin,*11) c Broadcast the order to compute internal coordinates to the slaves. if (nfgtasks.gt.1) & call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR) call int_from_cart1(.false.) else read (intin,'(i5)',end=1100,err=1100) iconf call read_angles(intin,*11) call geom_to_var(nvar,varia) call chainbuild endif write (iout,'(a,i7)') 'Conformation #',iconf call etotal(energy(0)) call briefout(iconf,energy(0)) call enerprint(energy(0)) etot=energy(0) if (refstr) then call rms_nac_nnc(rms,frac,frac_nn,co,.true.) call calc_tmscore(tm,.true.) write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot, & rms,frac,frac_nn,co,tm else write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot endif enddo 1100 continue goto 1101 endif mm=0 imm=0 nft=0 ene0=0.0d0 n=0 iconf=0 do while (.not. eof) mm=mm+1 if (mm.lt.nodes) then if (read_cart) then read (intin,'(e15.10,e15.5)',end=11,err=11) time,ene call read_x(intin,*11) c Broadcast the order to compute internal coordinates to the slaves. if (nfgtasks.gt.1) & call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR) call int_from_cart1(.false.) else read (intin,'(i5)',end=11,err=11) iconf call read_angles(intin,*11) call geom_to_var(nvar,varia) call chainbuild endif n=n+1 write (iout,*) 'Conformation #',iconf,' read' imm=imm+1 ind(1)=1 ind(2)=n ind(3)=0 ind(4)=0 ind(5)=0 ind(6)=0 ene0=0.0d0 call mpi_send(ind,6,mpi_integer,mm,idint,CG_COMM, * ierr) call mpi_send(varia,nvar,mpi_double_precision,mm, * idreal,CG_COMM,ierr) call mpi_send(ene0,1,mpi_double_precision,mm, * idreal,CG_COMM,ierr) c print *,'task ',n,' sent to worker ',mm,nvar else call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint, * CG_COMM,muster,ierr) man=muster(mpi_source) c print *,'receiving result from worker ',man,' (',iii1,iii,')' call mpi_recv(varia,nvar,mpi_double_precision, * man,idreal,CG_COMM,muster,ierr) call mpi_recv(ene,1, * mpi_double_precision,man,idreal, * CG_COMM,muster,ierr) call mpi_recv(ene0,1, * mpi_double_precision,man,idreal, * CG_COMM,muster,ierr) c print *,'result received from worker ',man,' sending now' call var_to_geom(nvar,varia) call chainbuild call etotal(energy(0)) iconf=ind(2) write (iout,*) write (iout,*) write (iout,*) 'Conformation #',iconf,ind(5) etot=energy(0) call enerprint(energy(0)) call briefout(iconf,etot) if (refstr) then call rms_nac_nnc(rms,frac,frac_nn,co,.true.) call calc_tmscore(tm,.true.) write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot, & rms,frac,frac_nn,co,tm else write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot endif imm=imm-1 if (read_cart) then read (intin,'(e15.10,e15.5)',end=1101,err=1101) time,ene call read_x(intin,*11) c Broadcast the order to compute internal coordinates to the slaves. if (nfgtasks.gt.1) & call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR) call int_from_cart1(.false.) else read (intin,'(i5)',end=1101,err=1101) iconf call read_angles(intin,*11) call geom_to_var(nvar,varia) call chainbuild endif n=n+1 write (iout,*) 'Conformation #',iconf,' read' imm=imm+1 ind(1)=1 ind(2)=n ind(3)=0 ind(4)=0 ind(5)=0 ind(6)=0 call mpi_send(ind,6,mpi_integer,man,idint,CG_COMM, * ierr) call mpi_send(varia,nvar,mpi_double_precision,man, * idreal,CG_COMM,ierr) call mpi_send(ene0,1,mpi_double_precision,man, * idreal,CG_COMM,ierr) nf_mcmf=nf_mcmf+ind(4) nmin=nmin+1 endif enddo 11 continue do j=1,imm call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint, * CG_COMM,muster,ierr) man=muster(mpi_source) call mpi_recv(varia,nvar,mpi_double_precision, * man,idreal,CG_COMM,muster,ierr) call mpi_recv(ene,1, * mpi_double_precision,man,idreal, * CG_COMM,muster,ierr) call mpi_recv(ene0,1, * mpi_double_precision,man,idreal, * CG_COMM,muster,ierr) call var_to_geom(nvar,varia) call chainbuild call etotal(energy(0)) iconf=ind(2) write (iout,*) write (iout,*) write (iout,*) 'Conformation #',iconf,ind(5) etot=energy(0) call enerprint(energy(0)) call briefout(iconf,etot) if (refstr) then call rms_nac_nnc(rms,frac,frac_nn,co,.true.) call calc_tmscore(tm,.true.) write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot, & rms,frac,frac_nn,co,tm else write (istat,'(i5,100(f12.3))') iconf, & (energy(print_order(i)),i=1,nprint_ene),etot endif nmin=nmin+1 enddo 1101 continue do i=1, nodes-1 ind(1)=0 ind(2)=0 ind(3)=0 ind(4)=0 ind(5)=0 ind(6)=0 call mpi_send(ind,6,mpi_integer,i,idint,CG_COMM, * ierr) enddo return end c---------------------------------------------------------------------------