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usage: tios-config [-h]

Create or modify the *tios* configuration file

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usage: tios-passwd [-h]

Change you *tios* password

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usage: tios-ls [-a]

List simulations in the *tios* database

Arguments:
  -a, --all     List jobs for all users, not just yourself.

Output:         One line per job, Fields are:
                    Job_id      6-character ID of the job, as set by tios-wrap.
                    Title       Descriptive title, as provided to tios-wrap.
                    Timepoint   Number of ps the simulation has been running for in total
                    Username    Name of the submitter as set by tios-config.
                    Status      Current status of the job.
                    Last_update Last time the simulation data was updated.

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usage: tios-info [-h] id

print information regarding a tios simulation

positional arguments:
  id          ID of tios simulation

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usage: tios-collect [-h] [-o TRAJFILE] [-l LOGFILE] [-p PDB] [-v]
                    [-t TIME_PERIOD] [-i INTERVAL] [-n FIRSTN] [-V]
                    id

Connect to a *tios* stream and download data

positional arguments:
  id                    tios id of the job to collect data from

optional arguments:
  -h, --help            show this help message and exit
  -o TRAJFILE, --trajfile TRAJFILE
                        name of trajectory file
  -l LOGFILE, --logfile LOGFILE
                        name of log file
  -p PDB, --pdb PDB     write a .pdb file to complement the trajectory
  -v, --verbose         display info as collection progresses
  -t TIME_PERIOD, --time_period TIME_PERIOD
                        time period over which to collect data (in ps or ns)
  -i INTERVAL, --interval INTERVAL
                        time interval between snapshots (in ps or ns)
  -n FIRTSTN, --firstn FIRSTN
                        include only these first N atoms in the trajectory file
  -V, --version         show program's version number and exit

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usage: tios-download [-h] id

Download copies of the simulation files (for Gromacs, .tpr and possibly .cpt files)

positional arguments:
  id          ID of *tios* simulation

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usage: tios-restart ID [-p PREAMBLE] [-e EXTRA_ARGS] [-r TRATE]

Connect to a stopped *tios* simulation and restart from where it left off.

Arguments:
  ID             The *tios* ID of the simulation to restart
  -p PREAMBLE, --preamble PREAMBLE
                 preamble for command line (e.g. mpirun)
  -e EXTRA_ARGS, --extra_args EXTRA_ARGS
                 extra arguments at end of command line (e.g. -maxh 24)
  -r TRATE, --trate TRATE
                 Sampling interval in ps

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usage: tios-cp ID [-t TITLE] 

Create a copy of a *tios* simulation (which may be currently running, or not), starting from the current coordinates

Arguments:
  ID             The *tios* ID of the simulation to clone from
  -t TITLE, --title TITLE
                 New title for the cloned simulation (else the parent's title is used)

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usage: tios-stop [-h] [-V] id

Stop a *tios* simulation remotely

positional arguments:
  id             tios id of the job

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usage: tios-submit [-h] [--title TITLE] [--selection SELECTION] [--trate TRATE] SIMCOMMAND

Arguments:
  -t TITLE, --title TITLE
                        descriptive title for the simulation
  -n FIRSTN, --firstn FIRSTN
                        store the first N (most interesting atoms e.g. solute?) separately. 
                        Can improve receiver performance
  -r TRATE, --trate TRATE
                        interval (in ps) between frames
positional arguments:
  SIMCOMMAND   The command that, by itself, would have been used to run the simulation job conventionally.
               Do not enclose this in quotes.

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usage: tios-add_user USERNAME PASSWORD

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usage: tios-remove_user USERNAME

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usage: tios-dockerhub_start ADMIN_USERNAME ADMIN_PASSWORD

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usage: tios-dockerhub_stop