NAME

       CPPTRAJ: - fast, parallelized molecular dynamics trajectory data analysis

SYNOPSIS

       cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]

DESCRIPTION

              [-ya  <args>]  [-xa  <args>] [<file>] [-c <reference>] [-d <datain>] [-w <dataout>]
              [-o  <output>]  [-h  |  --help]  [-V  |   --version]   [--defines]   [-debug   <#>]
              [--interactive]  [--log  <logfile>] [-tl] [-ms <mask>] [-mr <mask>] [--mask <mask>]
              [--resmask <mask>] [--rng {marsaglia|stdlib|mt|pcg32|xo128}]

       -p <Top0>
              : * Load <Top0> as a topology file.

       -i <Input0>
              : * Read input from file <Input0>.

       -y <trajin>
              : * Read from trajectory file <trajin>; same as input 'trajin <trajin>'.

       -x <trajout>
              : * Write trajectory file <trajout>; same as input 'trajout <trajout>'.

       -ya <args>
              : * Input trajectory file arguments.

       -xa <args>
              : * Output trajectory file arguments.

       <file> : * A topology, input trajectory, or file containing cpptraj input.

       -c <reference>
              :  *  Read  <reference>  as  reference  coordinates;  same  as   input   'reference
              <reference>'.

       -d <datain>
              : * Read data in from file <datain> ('readdata <datain>').

       -w <dataout>
              : Write data from <datain> as file <dataout> ('writedata <dataout>).

       -o <output>
              : Write CPPTRAJ STDOUT output to file <output>.

       -h | --help
              : Print command line help and exit.

       -V | --version
              : Print version and exit.

       --defines
              : Print compiler defines and exit.

       -debug <#>
              : Set global debug level to <#>; same as input 'debug <#>'.

       --interactive
              : Force interactive mode.

       --log <logfile>
              : Record commands to <logfile> (interactive mode only). Default is 'cpptraj.log'.

       -tl    : Print length of all input trajectories specified on the command line to STDOUT.

       -ms <mask>
              : Print selected atom numbers to STDOUT.

       -mr <mask>
              : Print selected residue numbers to STDOUT.

       --mask <mask>
              : Print detailed atom selection to STDOUT.

       --resmask <mask> : Print detailed residue selection to STDOUT.

       --rng <type>
              : Change default random number generator.

              * Denotes flag may be specified multiple times.