Ubuntu Manpage: replica_exchange - Work Queue application for running replica exchange simulations using

Provided by: coop-computing-tools_7.0.22-1ubuntu1_amd64

NAME

       replica_exchange  -  Work Queue application for running replica exchange simulations using
       ProtoMol

SYNOPSIS

       replica_exchange  [options]  <pdb_file>  <psf_file>   <par_file>   <min_temp>   <max_temp>
       <num_replicas>

DESCRIPTION

replica_exchange is a Work Queue application for running replica exchange simulations
using the ProtoMol simulation package. The application supports both barrier and non-
barrier based runs.

The barrier based run transfers the configuration files and input data for each replica to
the connected work_queue_worker() instances, runs the ProtoMol simulation package, and
gathers the output, at each Monte Carlo step. It waits for the completion of simulation of
all replicas at each step before proceeding to the next step and, therefore, incorporates
a barrier at each step. At the end of every step, it randomly picks two neigboring
replicas, applies the metropolis criterion, and if it is satisfied, swaps the parameters
of the two replicas and continues simulations.

The non-barrier based run is equivalent to the barrier run in the output and results
produced. However, it avoids the use of a barrier by running multiple monte carlo steps
for each replica until that replica is picked to attempt an exchange. By default, the
application will run using this non-barrier implementation.

The pdb_file, psf_file, and par_file arguments specify the input files required for the
simulation run. The min_temp and max_temp specify the temperature range in which the
replicas are simulated. The number of replicas simulated is given by num_replicas.

replica_exchange can be run on any machine accesible to work_queue_worker instances.

OPTIONS

        -n <name>
              Specify a project name for using exclusive work_queue_worker instances.

        -x <filename>
              Specify the name of the xyz file for output.

        -d <filename>
              Specify the name of the dcd file for output.

        -m <number>
              Specify the number of monte carlo steps. Default = 100.

        -s <number>
              Specify the number of molecular dynamics steps. Default = 10000.

        -p <path>
              Specify path for storing output files.

        -q    Assign closer temperature values to replicas in the first and last quartile.

        -i    Assume ProtoMol is installed and available in PATH on worker site.

        -b    Use barrier in waiting for all replicas to finish  their  steps  before  attempting
              exchange.

        -l    Print debuggging information.

        -h    Show this help message.

EXIT STATUS

       On success, returns zero.  On failure, returns non-zero.

ENVIRONMENT VARIABLES

       If  the cctools are installed in a non-system directory, such as your home directory, then
       you must set the PYTHONPATH environment so that the workqueue python module can be  found.
       For example:

               % setenv PYTHONPATH $HOME/cctools/lib/python2.4/site-packages

EXAMPLES

       To run a replica exchange experiment with 84 replicas in the temperature range 278 to 400K
       using the sample input files:

               % replica_exchange ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84

       To run a replica exchange experiment, with project name ReplExch,  over  250  Monte  Carlo
       steps  running  1000 molecular dynamics steps and involving 84 replicas in the temperature
       range 278 to 400K using the sample input files:

               % replica_exchange -N ReplExch -m 250 -s 1000 ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp 278 400 84

COPYRIGHT

       The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas  Thain  and  Copyright
       (C)  2005-2015  The  University of Notre Dame.  This software is distributed under the GNU
       General Public License.  See the file COPYING for details.