Difference between revisions of "gorex.pl"

Revision as of 18:10, 26 November 2008

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-help: usage information

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-== Description ==
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-This script is used to run replica exchange simulations for Ca-only Go-models based
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-on the Karanicolas and Brooks <a href="http://www.mmtsb.org/webservices/gomodel.html" target=cpar>
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-Go-model Builder</a>. In most parallel
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-environments it will start the replica exchange server automatically. The
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-options <B>-n</B>, <B>-par</B>, <B>-temp</B>, <B>-condfile</B>, <B>-ens</B>,
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-<B>-ensdir</B> are available as in <docmark>rexserver.pl</docmark>.
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-Alternatively, it can connect to an external replica exchange server
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-if its address, port, and ID are given with <B>-rserv</B>. In that case
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-<B>-jobs</B> may be used to run only some of the temperature windows instead
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-of all windows if multiple clients are launched on different machines.<BR>
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-For shared memory environments the option <B>-cpus</B> can be used
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-to specify a smaller number of CPUs than temperature windows if necessary
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-due to computational restraints. A host file can be given with
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-<B>-hosts</B> for automatic remote submission in a distributed environment.
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-(see <docmark>calcprop.pl</docmark> for a more detailed explanation).<BR>
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-In order to contact the server from an external program (e.g. for monitoring
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-purposes) the server ID is required. The option
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-<B>-saveid</B> is available to write this server information to a file.
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-<BR>
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-The intial input PDB and parameter/toplology files for each MD simulation are given by the
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-last command line argument in the form <i>PREFIX</i>, where this is the identifier following
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-the GO_<i>PREFIX</i> in the files returned by the Go Builder.<BR>
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-Additionally, different PDB coordinate files can be can be used to start each simulation.
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-They are read from an external file that is given with
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-<B>-f</B>.<BR>
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-The remaining parameters are used to control the MD simulations. Parameters
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-that can be given with <B>-mdpar</B> are shown
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-<A HREF="http://www.mmtsb.org/cgi-bin/charmmpar" TARGET=cpar>here</A>.<BR>
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-Further options given with
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-<B>-mdopt</B> control whether a trajectory or energy file is written out
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-(<font color=#508060>[no]trajout</font> and <font color=#508060>[no]enerout</font>).<BR>
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-The simulation protocol can be further customized by providing CHARMM commands
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-through external files. This can be done with <B>-custom</B> which expects a keyword
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-and a file name as arguments. The keyword is used to specify when the custom
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-command sequence should be inserted in the standard protocol. If <font color=#508060>setup</font>
-is used the commands will be sent to CHARMM only once during the initial setup
-phase. If the keywords <font color=#508060>pre</font> or <font color=#508060>post</font> the commands will
-be executed before or after the dynamics command, respectively. These keywords
-can be further qualified with <font color=#508060>:init</font>, <font color=#508060>:equi</font>, and <font color=#508060>:prod</font>
-corresponding to the replica exchange cycle modes to allow custom equilibration
-protocols.<BR>
-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
-energy log file is generated with <B>-elog</B>.
 == Options ==

Difference between revisions of "gorex.pl"

Revision as of 18:10, 26 November 2008

Options

Examples