aarex.pl - Revision history

Edit: /* Examples */

2009-07-31T02:37:22Z

Examples

Edit: /* Options */

2009-07-31T02:31:43Z

Options

Edit: /* Description */

2009-07-31T02:30:01Z

Description

Edit: /* Options */

2009-07-31T02:29:07Z

Options

Edit: /* Options */

2009-07-29T15:42:38Z

Options

Edit: /* Options */

2009-07-29T15:42:11Z

Options

Edit: /* Options */

2009-07-29T15:28:11Z

Options

Edit: /* Options */

2009-07-29T04:56:56Z

Options

Edit: /* Options */

2009-07-29T04:12:35Z

Options

Edit: /* Description */

2009-07-29T04:01:40Z

Description

@@ Line 123: / Line 123: @@
 <mmtsbToolExample cmd="aarex.pl" set="/apps/mmtsb/bench/aarex.pl-test/test9"></mmtsbToolExample>
-<span style="color:#800000">aarex.pl -mp -hosts hostlist -n 1000 -charmmlog logfile -par archive,natpdb=init.pdb -temp 24:298:450 -dir phmd_ph3
+<mmtsbToolExample cmd="aarex.pl" set="test10"></mmtsbToolExample>
-with [[gbsw_setup.str]], [[phmd-g5.in]] and<br>
+with [[gbsw_setup.str]], [[phmd-g5.in]] and a <b>hostlist</b> file that contains the names of available nodes.

@@ Line 73: / Line 73: @@
 ; -mdpar CHARMMparams : use specified [[CHARMM_Parameters]].  It should be noted that the default CHARMM parameter values for aarex.pl may be different for those of mdCHARMM.pl (i.e. cutnb, cuton, cutoff).  Thus it is always better to specify your CHARMM parameters.
 ; -mdopt key=value[,...] : CHARMM simulation options
-; -l refPDB min&#58;max[=min&#58;max] :
+; -l refPDB min&#58;max[=min&#58;max] : limit sampling to specified residue range while restraining structure to reference PDB otherwise
 ; -cons [ca|cb|cab|heavy ref|self min&#58;max[_force][=...] : apply a harmonic restraint to all specified atoms in a given range
 ; -opt file : options file
-; -custom :
+; -custom setup|pre|post[&#58;init|equi|prod] file : provide custom files to be loaded by CHARMM at different steps of the replica exchange run
 ; -dir directory : data directory
 ; -ens tag : store structures in an ensemble using the given tag name
 ; -ensdir dir : store structures in an ensemble using the given directory name
 ; -mpirun -n hosts mpirunexec : for parallel CHARMM executables using mpirun, specify the number of CPUs per replica, a host file, and the path to mpirun
 ; -charmmexec charmmexec : use CHARMM executable specified in given path

@@ Line 9: / Line 9: @@
 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 [[rexserver.pl]].
+<B>-ensdir</B> are available as in [[rexserver.pl]].<BR>
 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
@@ Line 19: / Line 21: @@
 <B>-hosts</B> for automatic remote submission in a distributed environment.
 (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 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 [[CHARMM_Parameters|here]].<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
@@ Line 40: / Line 47: @@
 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
@@ Line 50: / Line 58: @@
 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

@@ Line 58: / Line 58: @@
 ; -help : usage information
 ; -n runs : specifies the number of replica exchange cycles
-; -par :
+; -par key=value[....] : replica exchange simulation parameters
-; -temp nwin&#58;min&#58;max : specifies the number of replicas followed by the minimum and maximum temperatures
+; -temp nwin&#58;min&#58;max : number of replicas followed by the minimum and maximum temperatures
-; -condfile file : specifies a replica exchange [[Replica Exchange Condition File Examples|condition file]]
+; -condfile file : replica exchange [[Replica Exchange Condition File Examples|condition file]]
-; -f file : specifies a list of starting structures
+; -f file : list of starting structures
 ; -mdpar CHARMMparams : use specified [[CHARMM_Parameters]].  It should be noted that the default CHARMM parameter values for aarex.pl may be different for those of mdCHARMM.pl (i.e. cutnb, cuton, cutoff).  Thus it is always better to specify your CHARMM parameters.
-; -mdopt :
+; -mdopt key=value[,...] : CHARMM simulation options
 ; -l refPDB min&#58;max[=min&#58;max] :
 ; -cons [ca|cb|cab|heavy ref|self min&#58;max[_force][=...] : apply a harmonic restraint to all specified atoms in a given range
-; -opt optionsfile :
+; -opt file : options file
 ; -custom :
-; -dir workdir :
+; -dir directory : data directory
 ; -ens tag : store structures in an ensemble using the given tag name
 ; -ensdir dir : store structures in an ensemble using the given directory name

@@ Line 62: / Line 62: @@
 ; -condfile file : specifies a replica exchange [[Replica Exchange Condition File Examples|condition file]]
 ; -f file : specifies a list of starting structures
-; -mdpar CHARMMparams : use specified [[CHARMM_Parameters]].  It should be noted that the default CHARMM parameter values for aarex.pl may be different for those of mdCHARMM.pl.  Thus it is always better to specify your CHARMM parameters.
+; -mdpar CHARMMparams : use specified [[CHARMM_Parameters]].  It should be noted that the default CHARMM parameter values for aarex.pl may be different for those of mdCHARMM.pl (i.e. cutnb, cuton, cutoff).  Thus it is always better to specify your CHARMM parameters.
 ; -mdopt :
 ; -l refPDB min&#58;max[=min&#58;max] :