constant_ph Command Help

Command: $SCHRODINGER/constant_ph

usage: 
Runs a constant-pH simulation. This only works with the S-OPLS forcefield.

* Run a new job:
    $SCHRODINGER/constant_ph input.mae -time 5000.0 -HOST <job-host> -JOBNAME <jobname> -titratable-site all

* Restart a previously interrupted job:
    $SCHRODINGER/constant_ph -HOST <job-host> -JOBNAME <jobname> -RESTART

* Extend a completed job:
    $SCHRODINGER/constant_ph -time 1000.0 -HOST <job-host> -JOBNAME <jobname> -extend

positional arguments:
  inp_file              A Maestro structure file

options:
  -h, --help            show this help message and exit
  -seed <integer>       Specify seed of pseudorandom number generator for
                        initial atom velocities. Default: 2014.
  -ppj PPJ              Specify number of processors per job, which strictly
                        corresponds to the number of CPUs to request. On all
                        standard cluster configurations, this will also
                        correspond to the number of GPUs requested per job, as
                        Desmond will use one GPU per CPU. Default: 1.
  -prepare              Do not run job. Only prepare multisim input files.
  -JOBNAME <string>     Specify the job name.
  -maxjob <integer>     Maximum number of simultaneous subjobs. Default: 0
                        (unlimited)
  -energy-groups        Compute energy groups during production simulations.
  -time <real>          The time (in ps) for the production simulation stage,
                        not including adaptive sampling. The total production
                        simulation time is given by <time> +
                        <adapt_iterations>*<adapt_interval>. Default: 5000.0.
  -ensemble {muVT|NPT|NVT}
                        Specify the ensemble class. Default: muVT.
  -titratable-site TITRATABLE_SITES
                        Specify the titratable site to consider in the format
                        'A:2B' or 'chain:resnum[inscode]'. If no insertion
                        code is present, just leave it off 'A:2'. '_' can be
                        used to indicate an blank chain letter in '_:2'. Only
                        ASP/CYS/GLU/HIS/LYS residues may be titrated. You may
                        pass in the argument multiple times for multiple
                        sites.
  -ph-lower-limit <real>
                        Set to the lower limit of pH's to run simulations at.
  -ph-upper-limit <real>
                        Set to the upper limit of pH's to run simulations at.
  -ph-interval <real>   Set to the interval in pH units to run the simulations
                        at.
  -modify-dihe          Scale the torsion energies in the perturbation region
                        to improve sampling.
  -extend               Run an extension for the original job.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
  -WAIT                 Do not return a prompt until the job completes.
  -LOCAL                Do not use a temporary directory for job files. Keep
                        files in the current directory.
  -D, -DEBUG            Show details of Job Control operation.
  -TMPDIR TMPDIR        The name of the directory used to store files
                        temporarily during a job.
  -SAVE                 Return zip archive of job directory at job completion.
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.

Standard Options:
  -RETRIES RETRIES      If a subjob fails for any reason, it will be retried
                        RETRIES times.
  -RESTART              Restart a previously failed job, utilizing any already
                        completed subjobs.