MMTSB
Tool Set Documentation

Difference between revisions of "aarex.pl"

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== Description ==
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This script is used to run replica exchange simulations. In most parallel
 
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>,
 
<B>-ensdir</B> are available as in <docmark>rexserver.pl</docmark>.
 
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
 
<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>
 
For shared memory environments the option <B>-cpus</B> 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
 
<B>-hosts</B> for automatic remote submission in a distributed environment.
 
(see <docmark>calcprop.pl</docmark> for a more detailed explanation).<BR>
 
In order to contact the server from an external program (e.g. for monitoring
 
purposes) the server ID is required. The option
 
<B>-saveid</B> is available to write this server information to a file.
 
<BR>
 
The intial input PDB files for each MD simulation are expected either as
 
the last command line arguments or from an external file that is given with
 
<B>-f</B>.<BR>
 
The remaining parameters are used to control the MD simulations. Parameters
 
that can be given with <B>-mdpar</B> are shown <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>.<BR>
 
The option <B>-l</B> is available to provide a list of residues and
 
a template PDB structure for loop modeling. Please note that with this
 
option RMSD values that are automatically calculated if a reference PDB structure
 
is given are also limited to only these residues.<BR>
 
Further options given with
 
<B>-mdopt</B> control whether a trajectory or restart file is written out
 
(<font color=#508060>[no]trajout</font> and <font color=#508060>[no]restout</font>), how many MD steps
 
are used (default: 1) for averaging the energy score used in the replica exchange
 
Metropolis criteria (<font color=#508060>avgener</font>), whether the rest of protein is
 
restrained outside the loop (<font color=#508060>[no]conslim</font>), and the maximum
 
restraint force (<font color=#508060>limforce</font>) and type of restrained atoms (<font color=#508060>limsel</font>)
 
in this case. Other restraints may be specified with <B>-cons</B>.<BR>
 
The simulation protocol can be further customized by providing CHARMM commands
 
through external files. This can be done with <B>-custom</B> 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 <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 ==
 
 
 
; -help : usage information
 
 
 
 
 
== Examples ==
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test1"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test2"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test3"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test4"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test5"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test6"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test7"></mmtsbToolExample>
 
The condition file looks the following:
 
<pre>
 
bias rg
 
298 force=1.25,target=18.0
 
298 force=0.60,target=9.0
 
298 force=0.60,target=13.0
 
298 force=0.75,target=14.0
 
</pre>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test8"></mmtsbToolExample>
 
with the following condition file:
 
<pre>
 
bias rg
 
298 force=1.00,target=15.0
 
298 force=0.60,target=12.0
 
320 force=0.60,target=12.0
 
320 force=1.00,target=15.0
 
</pre>
 
 
 
<mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test9"></mmtsbToolExample>
 

Revision as of 20:48, 16 May 2008

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