fold_alanin.conf

分子动力学计算程序

# 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 8
set min_temp 300
set max_temp 600
set steps_per_run 1000
set num_runs 10000
# 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 "alanin_base.namd"
set output_root "output/fold_alanin" ; # directory must exist

# the following used only by show_replicas.vmd
set psf_file "alanin.psf"
set initial_pdb_file "unfolded.pdb"
set fit_pdb_file "alanin.pdb"

set namd_bin_dir /Projects/namd2/bin/current/Linux64
set server_port 3177

# 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.

# 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] ]

# run jobs on local machine
# set spawn_namd_command \
#   [list spawn_namd_simple "[file join $namd_bin_dir namd2] +netpoll"]

# 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 ]