3. Getting Started

In this section we will briefly describe how RepEx can be invoked, how input and resource configuration files should be used.

3.1. Invoking RepEx

To run RepEx users need to use a command line tool corresponding to MD package kernel they intend to use. For example, if user wants to use Amber as MD kernel, she would use repex-amber command line tool. In addition to specifying an appropriate command line tool, user need to specify a resource configuration file and REMD simulation input file. The resulting invocation of RepEx should be:

repex-amber --input='tuu_remd_ace_ala_nme.json' --rconfig='stampede.json'

where:

--input= - specifies the REMD simulation input file

--rconfig= - specifies resource configuration file

Both REMD simulation input file and resource configuration file must conform to JSON format.

3.1.1. Resource configuration file

In resource configuration file must be provided the following parameters:

• resource - this is the name of the target machine. Currently supported machines are:

  local.localhost - your local system

  xsede.stampede - Stampede supercomputer at TACC

  xsede.supermic - SuperMIC supercomputer at LSU

  xsede.comet - Comet supercomputer at SDSC

  xsede.gordon - Gordon supercomputer at SDSC

  epsrc.archer - Archer supercomputer at EPCC

  ncsa.bw_orte - Blue Waters supercomputer at NCSA

• username - your username on the target machine

• project - your allocation on specified machine

• cores - number of cores you would like to allocate

• runtime - for how long you would like to allocate cores on target machine (in minutes).

In addition are provided the following optional parameters:

• queue - specifies which queue to use for job submission. Values are machine specific.
• cleanup - specifies if files on remote machine must be deleted. Possible values are: True or False

Example resource configuration file for Stampede supercomputer might look like this:

{
    "target": {
            "resource" : "xsede.stampede",
            "username" : "octocat",
            "project"  : "TG-XYZ123456",
            "queue"    : "development",
            "runtime"  : "30",
            "cleanup"  : "False",
            "cores"    : "16"
    }
}

3.1.2. REMD input file for Amber kernel

For use with Amber kernel, in REMD simulation input file must be provided the following parameters:

• re_pattern - this parameter specifies Replica Exchange Pattern to use, options are: S - synchronous and A - asynchronous
• exchange - this parameter specifies type of REMD simulation, for 1D simulation options are: T-REMD, S-REMD and US-REMD
• number_of_cycles - number of cycles for a given simulation
• number_of_replicas - number of replicas to use
• input_folder - path to folder which contains simulation input files
• input_file_basename - base name of generated input/output files
• amber_input - name of input file template
• amber_parameters - name of parameters file
• amber_coordinates - name of coordinates file
• replica_mpi - specifies if sander or sander.MPI is used for MD-step. Options are: True or False
• replica_cores - number of cores to use for MD-step for each replica, if replica_mpi is False this parameters must be equal to 1
• steps_per_cycle - number of simulation time-steps
• download_mdinfo - specifies if Amber .mdinfo files must be downloaded. Options are: True or False. If this parameter is ommited, value defaults to “True”
• download_mdout - specifies if Amber .mdout files must be downloaded. Options are: True or False. If this parameter is ommited, value defaults to “True”

Optional parameters are specific to each simulation type. Example REMD simulation input file for T-REMD simulation might look like this:

{
    "remd.input": {
            "re_pattern": "S",
            "exchange": "T-REMD",
            "number_of_cycles": "4",
            "number_of_replicas": "16",
            "input_folder": "t_remd_inputs",
            "input_file_basename": "ace_ala_nme_remd",
            "amber_input": "ace_ala_nme.mdin",
            "amber_parameters": "ace_ala_nme.parm7",
            "amber_coordinates": "ace_ala_nme.inpcrd",
            "replica_mpi": "False",
            "replica_cores": "1",
            "min_temperature": "300",
            "max_temperature": "600",
            "steps_per_cycle": "1000",
        "download_mdinfo": "True",
        "download_mdout" : "True",
    }
}