rexserver.pl - Revision history

Edit: /* Options */

2009-07-30T21:13:38Z

Options

Edit: /* Options */

2009-07-30T21:12:24Z

Options

Edit: /* Options */

2009-07-30T21:11:39Z

Options

Edit: /* Description */

2009-07-30T20:39:29Z

Description

Feig at 14:27, 12 August 2006

2006-08-12T14:27:53Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="rexserver.pl"></mmtsbToolUsage>

== Description ==

This script is used for manually starting a replica exchange server
for all-atom simulations. The utilities <docmark>aarex.pl</docmark>
or <docmark>latrex.pl</docmark>
can then be used to run clients connecting to the server.
Both of these scripts can launch the server automatically
depending on the parallel environment in which case the
server does not need to be started manually with this script. 
The following options are available: The number of desired
exchange steps is given with -n. For lattice replica exchange
simulations with MONSSTER the flag -monsster needs to
be specified. 
A number or parameters are set with -par. At the beginning of a
replica exchange simulation no exchange is done after the first few steps
to allow for equilibration. The parameter initruns is used
to control the number of the steps. After the initial equilibration
a second level equilibration is carried out for equilruns
steps that are not considered as part of the actual production run.
The client is notified of the current equilibration stage at each step
to also allow for special equilibration restraints during the
simulation. A reference structure for calculating RMSD values can
be given with natpdb. 
For loop modeling a fragment list and reference
structure may be provided with -l. 
The structures from the lowest temperature window (or first condition in
the condition file, see below) can be automatically
checked into an ensemble. The parameter savefreq determines
how often (in number of exchange steps) a conformation is saved while
the options -ens and -ensdir are used to set the ensemble
tag and directory, respectively. 
Temperature steps may be set by automatic assignement of exponentially
spaced temperatures between minimum and maximum values given with
-temp. For replica exchange simulations with more complicated replica
conditions a condition file has to be given with -condfile. In addition
to temperature other biasing conditions can include harmonic umbrella
potentials for different properties, e.g. for the radius of gyration.
Multiple bias conditions may be combined to achieve multidimensional replica
exchange simulations. In the condition file a line beginning
with the keyword bias is expected to describe any umbrella
biases that are to be applied, e.g. rg for radius of gyration.
For each replica a line beginning with cond
provides the temperature along with parameters for all biases such as force
constants and target values where the biasing potential is zero. Combinations
of multiple biases are possible but may be limited by CHARMM capabilities. 
If the replica exchange simulation is started from
initial structures, they are expected either as the last arguments or in
a list file given with -f. The given structures are assigned to
ascending temperature windows in the given order. If the same initial
structure is used for all temperature windows it is sufficient to
give it only once. For lattice simulations started from random chains
or restarted all-atom simulations initial files are not expected. 
A server log file can be requested with -log.

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="rexserver.pl" set="/apps/mmtsb/bench/rexserver.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="rexserver.pl" set="/apps/mmtsb/bench/rexserver.pl-test/test2"></mmtsbToolExample>

@@ Line 78: / Line 78: @@
 ; -condfile file : file with replica exchange conditions
 ; -log logfile : replica exchange log file
-; -serverid num : ?
+; -serverid num : start server with a specific ID (otherwise assigned randomly)
 == Examples ==

@@ Line 68: / Line 68: @@
 ; -help : usage information
 ; -n runs : number of cycles to run
-; -f listfile : ?
+; -f listfile : file with names of different initial structures for different replicas
 ; -dir directory : data directory
 ; -monsster : run replica exchange with MONSSTER

@@ Line 7: / Line 7: @@
 This script is used for manually starting a replica exchange server
-for all-atom simulations. The utilities <docmark>aarex.pl</docmark>
+for all-atom simulations. The utilities [[aarex.pl]]
-or <docmark>latrex.pl</docmark>
+or [[latrex.pl]]
 can then be used to run clients connecting to the server.
 Both of these scripts can launch the server automatically
@@ Line 17: / Line 17: @@
 simulations with MONSSTER the flag <B>-monsster</B> needs to
 be specified.<BR>
 A number or parameters are set with <B>-par</B>. At the beginning of a
 replica exchange simulation no exchange is done after the first few steps
@@ Line 27: / Line 28: @@
 simulation. A reference structure for calculating RMSD values can
 be given with <font color=#508060>natpdb</font>.<BR>
 For loop modeling a fragment list and reference
 structure may be provided with <B>-l</B>.<BR>
 The structures from the lowest temperature window (or first condition in
 the condition file, see below) can be automatically
@@ Line 35: / Line 38: @@
 the options <B>-ens</B> and <B>-ensdir</B> are used to set the ensemble
 tag and directory, respectively.<BR>
 Temperature steps may be set by automatic assignement of exponentially
 spaced temperatures between minimum and maximum values given with
@@ Line 49: / Line 53: @@
 constants and target values where the biasing potential is zero. Combinations
 of multiple biases are possible but may be limited by CHARMM capabilities.<BR>
 If the replica exchange simulation is started from
 initial structures, they are expected either as the last arguments or in
@@ Line 56: / Line 61: @@
 give it only once. For lattice simulations started from random chains
 or restarted all-atom simulations initial files are not expected.<BR>
 A server log file can be requested with <B>-log</B>.