unbinding_kinetics Command Help

Command: $SCHRODINGER/unbinding_kinetics

usage: 
Unbinding Kinetics is a workflow for sampling both unbinding pathways
and absolute residence times. The workflow runs in two stages.
First, Random Acceleration Molecular Dynamics (RAMD) is used
to sample exit pathways and their relative frequencies.
Then, Infrequent Metadynamics is used to sample unbinding events along
the most common exit pathway(s) and their associated timescales.

The workflow can be truncated to only run through the RAMD stage with
the -ramd-only flag.

* Run a new job:
    $SCHRODINGER/unbinding_kinetics input.mae -JOBNAME <jobname> -HOST <main-host> -SUBHOST <subhost>

positional arguments:
  inp_file              A Maestro structure file

options:
  -h, --help            show this help message and exit
  -ff {OPLS4|OPLS5}     Specify the forcefield to use. Default: OPLS4.
  -prepare              Do not run job. Only prepare multisim input files.
  -JOBNAME <string>     Specify the job name.
  -buffer <real>        Specify a larger buffer size (in Angstroms). Defaults:
                        5 in complex leg, 5 in solvent leg of protein-residue-
                        mutation FEP, 10 in solubility FEP, 10 in solvent leg
                        of other types of FEP, 10 for protein-protein
                        interactioncalculations, 8.0 for kinetics calculations
                        and 10.0 for kinetics calculations with membrane. The
                        custom value will be used only if it's greater than
                        the corresponding default values.
  -maxjob <integer>     Maximum number of simultaneous subjobs. Default: 0
                        (unlimited)
  -energy-groups        Compute energy groups during production simulations.
  -enable-metal-force-field
                        Enable metal support for the OPLS5 force field.
  -asl-receptor <string>
                        Atom selection language for the receptor. Default:
                        protein or dna or rna
  -asl-ligand <string>  Atom selection language for the ligand. Default:
                        ligand
  -custom-charge-mode {keep|clear|assign}
                        Set to "assign" to assign custom charges. Set to
                        "clear" to clear custom charges if present, without
                        reassigning. Set to "keep" to keep existing custom
                        charges if present. Default: assign
  -membrane {None|POPC-POPE_1-1|POPC|DMPC|POPE|DPPC|POPC-CLR_7-3|POPC-DPPC-CLR_2-2-1|POPC-CLR_1-1|POPC-CLR_9-1|POPC-SM-CLR_2-2-1|POPC-DMPC_1-1}
                        Use this option when working with a membrane-bound
                        receptor. The protocol will automatically add the
                        specified lipid patch. Ensure that the receptor's
                        orientation OPM-compatible. For more details, refer to
                        the Desmond Manual. Default: None
  -rmsd-cutoff <real>   RMSD cutoff to consider the ligand unbound in Å.
                        Default: 5.0
  -mindist-cutoff <real>
                        MinDist (minimum distance between ligand heavy atoms
                        and receptor carbon alphas) cutoff to consider the
                        ligand unbound in Å. Default: 8.0
  -stability-sim-time <sim-time>
                        Length of simulation (in ps) to establish the ligand's
                        stability within the binding pocket. A value of 0 will
                        skip the stability validation stage. Default: 10000

Random Acceleration MD Options:
  -ramd-only            Option to only run RAMD and not metadynamics. Default:
                        False
  -total-ramd-replicas <integer>
                        Number of RAMD simulations to submit. Default: 30
  -ramd-spring-fk <real>
                        Initial force constant for RAMD simulations in
                        kcal/mol/Ų. Default: 15.0
  -ramd-fk-increase-rate <real>
                        Rate at which the RAMD force constant increases in
                        kcal/mol/Ų/ns. Default: 0.005

Infrequent Metadynamics Options:
  -total-mtd-replicas <integer>
                        Number of infrequent metadynamics simulatinos to
                        submit. Default: 10
  -time <sim-time>      Specify maximum time (in ps) for the metadynamics
                        stage. Default: 200000
  -residence-time-cutoff <real>
                        Maximum accelerated time before metadynamics jobs are
                        terminated. Default: 1.00e+10
  -path-cv-z-wall <real>
                        Width of flat bottom restraints on the Z path CV which
                        measures distance from the path waypoints in Ų.
                        Default: 250.0

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:
  -SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"
                        Run the subjobs on the specified hosts. The driver is
                        run on the host specified with -HOST.
  -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.