gorex.pl - Revision history

Edit: /* Description */

2009-07-31T02:18:43Z

Description

Edit: /* Options */

2009-07-31T02:18:17Z

Options

Edit: /* Options */

2009-07-31T02:14:56Z

Options

Edit: /* Description */

2009-07-31T02:05:30Z

Description

Edit: /* Description */

2009-07-31T02:04:57Z

Description

Feig at 22:53, 7 January 2009

2009-01-07T22:53:55Z

217.167.7.6: boizZBQVShsq

2009-01-01T19:01:45Z

boizZBQVShsq

203.110.240.22: wQomKGIofBsbasxqwH

2009-01-01T18:57:41Z

wQomKGIofBsbasxqwH

213.34.199.200: gnMkbbXRdTBIhktKOG

2009-01-01T18:57:26Z

gnMkbbXRdTBIhktKOG

193.203.99.31: fZiQPsiKEuSbF

2009-01-01T18:56:24Z

fZiQPsiKEuSbF

@@ Line 40: / Line 40: @@
 energy file is written out
 (<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
 through external files. This can be done with <B>-custom</B> which expects a keyword

@@ Line 66: / Line 66: @@
 ; -ens tag : ensemble tag for storing conformations at lowest temperature
 ; -ensdir dir : ensemble directory
 == Examples ==

@@ Line 58: / Line 58: @@
 ; -help : usage information
+; -n runs : number of replica exchange cycles
 == Examples ==

@@ Line 29: / Line 29: @@
 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
-the GO_<i>PREFIX</i> in the files returned by the Go Builder.<BR>
+the GO_<i>PREFIX</i> 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
-<B>-f</B>.<BR>
+<B>-f</B>.
 The remaining parameters are used to control the MD simulations. Parameters
 that can be given with <B>-mdpar</B> are shown

@@ Line 7: / Line 7: @@
 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
 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>.
+<B>-ensdir</B> 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 <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>
+(see [[calcprop.pl]] 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 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
@@ Line 33: / Line 35: @@
 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>
+[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
 (<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
@@ Line 47: / Line 50: @@
 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

←Older revision		Revision as of 22:53, 7 January 2009
Line 1:		Line 1:
−	~~dummy~~	+	__NOTOC__
		+	== Usage ==
		+
		+	<mmtsbToolUsage cmd="gorex.pl"></mmtsbToolUsage>
		+
		+	== Description ==
		+
		+	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>
		+	Go-model Builder</a>. 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 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
		+	the GO_<i>PREFIX</i> in the files returned by the Go Builder.<BR>
		+	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
		+	<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>
		+	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>
		+	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 ==

←Older revision	Revision as of 19:01, 1 January 2009
(No difference)

←Older revision	Revision as of 18:57, 1 January 2009
(No difference)

←Older revision	Revision as of 18:56, 1 January 2009
(No difference)