Provided by: coop-computing-tools_9.9-2ubuntu3_amd64 bug

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) 2005-2019 The University of Notre  Dame.
       This  software  is distributed under the GNU General Public License.  See the file COPYING
       for details.

SEE ALSO

Cooperative Computing Tools DocumentationWork Queue User Manualwork_queue_worker(1)            work_queue_status(1)             work_queue_factory(1)
           condor_submit_workers(1) sge_submit_workers(1) torque_submit_workers(1)