Provided by: cpptraj_5.1.0+dfsg-4build2_amd64 
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.