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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
.TH CPPTRAJ: "1" "August 2022" "CPPTRAJ: Version V5.1.0 (GitHub)" "User Commands"
.SH NAME
CPPTRAJ: \- fast, parallelized molecular dynamics trajectory data analysis
.SH SYNOPSIS
.B cpptraj
[\fI\,-p <Top0>\/\fR] [\fI\,-i <Input0>\/\fR] [\fI\,-y <trajin>\/\fR] [\fI\,-x <trajout>\/\fR]
.SH DESCRIPTION
.IP
[\-ya <args>] [\-xa <args>] [<file>]
[\-c <reference>] [\-d <datain>] [\-w <dataout>] [\-o <output>]
[\-h | \fB\-\-help]\fR [\-V | \fB\-\-version]\fR [\-\-defines] [\-debug <#>]
[\-\-interactive] [\-\-log <logfile>] [\-tl]
[\-ms <mask>] [\-mr <mask>] [\-\-mask <mask>] [\-\-resmask <mask>]
[\-\-rng {marsaglia|stdlib|mt|pcg32|xo128}]
.TP
\fB\-p\fR <Top0>
: * Load <Top0> as a topology file.
.TP
\fB\-i\fR <Input0>
: * Read input from file <Input0>.
.TP
\fB\-y\fR <trajin>
: * Read from trajectory file <trajin>; same as input 'trajin <trajin>'.
.TP
\fB\-x\fR <trajout>
: * Write trajectory file <trajout>; same as input 'trajout <trajout>'.
.TP
\fB\-ya\fR <args>
: * Input trajectory file arguments.
.TP
\fB\-xa\fR <args>
: * Output trajectory file arguments.
.TP
<file>
: * A topology, input trajectory, or file containing cpptraj input.
.TP
\fB\-c\fR <reference>
: * Read <reference> as reference coordinates; same as input 'reference <reference>'.
.TP
\fB\-d\fR <datain>
: * Read data in from file <datain> ('readdata <datain>').
.TP
\fB\-w\fR <dataout>
: Write data from <datain> as file <dataout> ('writedata <dataout>).
.TP
\fB\-o\fR <output>
: Write CPPTRAJ STDOUT output to file <output>.
.TP
\fB\-h\fR | \fB\-\-help\fR
: Print command line help and exit.
.TP
\fB\-V\fR | \fB\-\-version\fR
: Print version and exit.
.TP
\fB\-\-defines\fR
: Print compiler defines and exit.
.TP
\fB\-debug\fR <#>
: Set global debug level to <#>; same as input 'debug <#>'.
.TP
\fB\-\-interactive\fR
: Force interactive mode.
.TP
\fB\-\-log\fR <logfile>
: Record commands to <logfile> (interactive mode only). Default is 'cpptraj.log'.
.TP
\fB\-tl\fR
: Print length of all input trajectories specified on the command line to STDOUT.
.TP
\fB\-ms\fR <mask>
: Print selected atom numbers to STDOUT.
.TP
\fB\-mr\fR <mask>
: Print selected residue numbers to STDOUT.
.TP
\fB\-\-mask\fR <mask>
: Print detailed atom selection to STDOUT.
.HP
\fB\-\-resmask\fR <mask> : Print detailed residue selection to STDOUT.
.TP
\fB\-\-rng\fR <type>
: Change default random number generator.
.IP
* Denotes flag may be specified multiple times.
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