usage: gorex.pl [options] PREFIX options: [-n runs] [-f listfile] [-dir workdir] [-par initruns=value,equilruns=value, [no]save,savebestfreq=value] [-temp nwin:min:max] [-condfile file] [-ens tag] [-ensdir dir] [PARALLELoptions] [-log file] [-elog file] [-charmmlog file] [-opt optionsfile] [-custom setup|pre|post[:init|equi|prod] file] [-mdpar steps=val,fbeta=val,timestep=val,outfrq=val,dynupdnb=val,dynupdimg=val] [-mdopt [no]trajout,[no]enerout]
This script is used to run replica exchange simulations for Ca-only Go-models based
on the Karanicolas and Brooks Go-model Builder. In most parallel
environments it will start the replica exchange server automatically. The
options -n, -par, -temp, -condfile, -ens,
-ensdir are available as in rexserver.pl.
Alternatively, it can connect to an external replica exchange server
if its address, port, and ID are given with -rserv. In that case
-jobs may be used to run only some of the temperature windows instead
of all windows if multiple clients are launched on different machines.
For shared memory environments the option -cpus can be used
to specify a smaller number of CPUs than temperature windows if necessary
due to computational restraints. A host file can be given with
-hosts for automatic remote submission in a distributed environment.
(see calcprop.pl for a more detailed explanation).
In order to contact the server from an external program (e.g. for monitoring
purposes) the server ID is required. The option
-saveid is available to write this server information to a file.
The intial input PDB and parameter/toplology files for each MD simulation are given by the
last command line argument in the form PREFIX, where this is the identifier following
the GO_PREFIX in the files returned by the Go Builder.
Additionally, different PDB coordinate files can be can be used to start each simulation.
They are read from an external file that is given with
The remaining parameters are used to control the MD simulations. Parameters
that can be given with -mdpar are shown
Further options given with -mdopt control whether a trajectory or
energy file is written out
([no]trajout and [no]enerout).
The simulation protocol can be further customized by providing CHARMM commands
through external files. This can be done with -custom which expects a keyword
and a file name as arguments. The keyword is used to specify when the custom
command sequence should be inserted in the standard protocol. If setup
is used the commands will be sent to CHARMM only once during the initial setup
phase. If the keywords pre or post the commands will
be executed before or after the dynamics command, respectively. These keywords
can be further qualified with :init, :equi, and :prod
corresponding to the replica exchange cycle modes to allow custom equilibration
The option -log is available to request a server log file. A CHARMM log file is generated for each client if -charmmlog is given, an energy log file is generated with -elog.
- usage information
- -n runs
- number of replica exchange cycles
- -f listfile
- list of initial files for different replicas
- -dir directory
- data directory
- -par key=value[,...]
- replica exchange simulation parameters
- -temp nwin:min:max
- number and range of temperature replicas
- -condfile cond
- conditions file
- -ens tag
- ensemble tag for storing conformations at lowest temperature
- -ensdir dir
- ensemble directory
- -log file
- replica exchange log file
- -elog file
- energy log file
- -charmmlog file
- CHARMM log file
- -opt file
- options file
- -custom setup|pre|post[:init|equi|prod] file
- custom files for CHARMM
- -mdpar key=value[,...]
- CHARMM simulation parameters
- -mdopt key=value[,...]
- CHARMM simulation options