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.

CPPTRAJ: Version V5.1.0 (GitHub)                   August 2022                                       CPPTRAJ:(1)