MMTSB
Tool Set Documentation

Difference between revisions of "gorex.pl"

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This script is used to run replica exchange simulations for Ca-only Go-models based
 
This script is used to run replica exchange simulations for Ca-only Go-models based
on the Karanicolas and Brooks <a href="http://mmtsb.scripps.edu/webservices/gomodel.html" target=cpar>
+
on the Karanicolas and Brooks [http://www.mmtsb.org/webservices/gomodel.html Go-model Builder]. In most parallel
Go-model Builder</a>. In most parallel
 
 
environments it will start the replica exchange server automatically. The
 
environments it will start the replica exchange server automatically. The
 
options <B>-n</B>, <B>-par</B>, <B>-temp</B>, <B>-condfile</B>, <B>-ens</B>,
 
options <B>-n</B>, <B>-par</B>, <B>-temp</B>, <B>-condfile</B>, <B>-ens</B>,
<B>-ensdir</B> are available as in <docmark>rexserver.pl</docmark>.
+
<B>-ensdir</B> are available as in [[rexserver.pl]].
 
Alternatively, it can connect to an external replica exchange server
 
Alternatively, it can connect to an external replica exchange server
 
if its address, port, and ID are given with <B>-rserv</B>. In that case
 
if its address, port, and ID are given with <B>-rserv</B>. In that case
 
<B>-jobs</B> may be used to run only some of the temperature windows instead
 
<B>-jobs</B> may be used to run only some of the temperature windows instead
 
of all windows if multiple clients are launched on different machines.<BR>
 
of all windows if multiple clients are launched on different machines.<BR>
 +
 
For shared memory environments the option <B>-cpus</B> can be used
 
For shared memory environments the option <B>-cpus</B> can be used
 
to specify a smaller number of CPUs than temperature windows if necessary
 
to specify a smaller number of CPUs than temperature windows if necessary
 
due to computational restraints. A host file can be given with
 
due to computational restraints. A host file can be given with
 
<B>-hosts</B> for automatic remote submission in a distributed environment.
 
<B>-hosts</B> for automatic remote submission in a distributed environment.
(see <docmark>calcprop.pl</docmark> for a more detailed explanation).<BR>
+
(see [[calcprop.pl]] for a more detailed explanation).<BR>
 +
 
 
In order to contact the server from an external program (e.g. for monitoring
 
In order to contact the server from an external program (e.g. for monitoring
 
purposes) the server ID is required. The option
 
purposes) the server ID is required. The option
 
<B>-saveid</B> is available to write this server information to a file.
 
<B>-saveid</B> is available to write this server information to a file.
 
<BR>
 
<BR>
 +
 
The intial input PDB and parameter/toplology files for each MD simulation are given by the
 
The intial input PDB and parameter/toplology files for each MD simulation are given by the
 
last command line argument in the form <i>PREFIX</i>, where this is the identifier following
 
last command line argument in the form <i>PREFIX</i>, where this is the identifier following
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The remaining parameters are used to control the MD simulations. Parameters
 
The remaining parameters are used to control the MD simulations. Parameters
 
that can be given with <B>-mdpar</B> are shown
 
that can be given with <B>-mdpar</B> are shown
<A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>.<BR>
+
[http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters here].<BR>
Further options given with
+
 
<B>-mdopt</B> control whether a trajectory or energy file is written out
+
Further options given with <B>-mdopt</B> control whether a trajectory or  
 +
energy file is written out
 
(<font color=#508060>[no]trajout</font> and <font color=#508060>[no]enerout</font>).<BR>
 
(<font color=#508060>[no]trajout</font> and <font color=#508060>[no]enerout</font>).<BR>
 
The simulation protocol can be further customized by providing CHARMM commands
 
The simulation protocol can be further customized by providing CHARMM commands
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corresponding to the replica exchange cycle modes to allow custom equilibration
 
corresponding to the replica exchange cycle modes to allow custom equilibration
 
protocols.<BR>
 
protocols.<BR>
 +
 
The option <B>-log</B> is available to request a server log file. A CHARMM
 
The option <B>-log</B> is available to request a server log file. A CHARMM
 
log file is generated for each client if <B>-charmmlog</B> is given, an
 
log file is generated for each client if <B>-charmmlog</B> is given, an

Revision as of 02:04, 31 July 2009

Usage

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]

Show source


Description

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 -f.
The remaining parameters are used to control the MD simulations. Parameters that can be given with -mdpar are shown here.

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 protocols.

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.

Options

-help 
usage information


Examples