watermap Command Help

Command: $SCHRODINGER/watermap

WaterMap workflow driver
Built upon Multisim workflow engine

WaterMap runs Desmond MD simulations followed by a water thermodynamics analysis
stage.

Usage:
* To run a WaterMap job, execute the following:
  $SCHRODINGER/watermap [options] <-m .msj_file> <.cms_or_.mae_file>

* To restart a previous WaterMap job, execute the following:
  $SCHRODINGER/watermap [options] <-RESTART multisim_checkpoint_file>
  You may need to specify the '-d' option followed by the .tgz file of the
  last completed stage.

Frequently used options:
 -m       <input_file>   input .msj file defining the WaterMap workflow
 -d       <input_file>   data file from the previous job which will have a
                         .tgz suffix. This option should be used only when
                         restarting a job with multisim checkpoint file
 -c       <input_file>   alter configuration parameters for a family of stages
 -o       <output_file>  output .cms or .mae file. This file can be analyzed
                         with into Maestro
 -cpu     <number>       number of CPUs for each subjob.
 -notify  <email_addr>   send a notification email when this job terminates.
 -nopref                 ignore the multisim preferences.
 -probe                  probe a checkpoint file and quit
 -JOBNAME <job_name>     name of this multisim job
 -HOST    <host_name>    host machine to run the multisim master job (default is
                         localhost)
 -SUBHOST <subhost_name> Host machine to run the multisim GPU subjobs. If not
                         specified, the machine specified by the -HOST argument
                         will be used to run the subjobs. If the host and
                         subhost are the same, the subjobs will be run in
                         "umbrella" mode, in which subjobs are not submitted to
                         the queuing system.
 -RESTART <input_file>   restart WaterMap job with a specified multisim checkpoint
                         file
 -h       {topic}        show help and quit. User can optionally specify a topic
                         for help. Valid topics are the following: @all, @doc,
                         @<flag> (where <flag> represents the flag of any valid
                         option, e.g., @-cpu, @-help), @examples, and @deprecated.
                         For more detail see help of the '@-help' topic.

See "$SCHRODINGER/watermap -h @examples" for command examples.