# configuration for replica exchange scripts # run simulation: tclsh ../replica_exchange.tcl fold_alanin.conf # to continue: tclsh ../replica_exchange.tcl restart_1.conf # view in VMD: source fold_alanin.conf; source ../show_replicas.tcl # add continued: source restart_1.conf; source ../show_replicas.tcl # show both: vmd -e load_all.vmd set num_replicas 10 set min_temp 300 set max_temp 400 set steps_per_run 1000 set num_runs 100 # num_runs should be divisible by runs_per_frame * frames_per_restart set runs_per_frame 10 set frames_per_restart 10 set namd_config_file "synuclein_base.namd" set output_root "output/fold_synuclein" ; # directory must exist # the following used only by show_replicas.vmd set psf_file "test_xplor.psf" set initial_pdb_file "test.pdb" set fit_pdb_file "test.pdb" set namd_bin_dir /home/datouyu/software/namd_icc_nc set server_port 3177 # set server_port 0 ;# use file-based transport # Uncomment and/or modify a spawn command below based on your environment # NOTE: Running namd2 through charmrun interferes with socket connections; # run the namd2 binary directly (in standalone mode). MPI might work. # run jobs on local machine set spawn_namd_command \ [list spawn_namd_simple "[file join $namd_bin_dir namd2] +netpoll +idlepoll"] # [list spawn_namd_simple "[file join $namd_bin_dir charmrun] ++local +p2 [file join $namd_bin_dir namd2] +idlepoll +netpoll"] # [list spawn_namd_simple "[file join $namd_bin_dir namd2] +idlepoll +netpoll"] # [list spawn_namd_simple "[file join $namd_bin_dir charmrun] ++local +p2 [file join $namd_bin_dir namd2] +netpoll +idlepoll"] # [list spawn_namd_simple "[file join $namd_bin_dir namd2] +netpoll"] # run on Cray XT3 # set namd_bin_dir /usr/users/7/jphillip/NAMD_2.6_CRAY-XT3/ # set server_port 0 ;# use file-based transport # set spawn_namd_command \ # [list spawn_namd_crayxt "-small_pages [file join $namd_bin_dir namd2]" ] # spread jobs across a given set of machines # set spawn_namd_command \ # [list spawn_namd_ssh "cd [pwd]; [file join $namd_bin_dir namd2] +netpoll" \ # [list beirut belfast] ] # spread jobs across machines assigned by queueing system # set spawn_namd_command \ # [list spawn_namd_ssh "cd [pwd]; [file join $namd_bin_dir namd2] +netpoll" \ # $env(LSB_HOSTS) ] # spread jobs across machines assigned by queueing system # set spawn_namd_command \ # [list spawn_namd_ssh "cd [pwd]; [file join $namd_bin_dir namd2] +netpoll" \ # [read [open $env(HOST_FILE) "r"]] ] # run parallel jobs - this may or may not work # set spawn_namd_command \ # [list spawn_namd_parallel # "cd [pwd]; $namd_bin_dir/charmrun $namd_bin_dir/namd2 +netpoll" \ # $env(LSB_HOSTS) 1 ]