---
name: "cpptraj"
section: "1"
platform: "linux"
package: "cpptraj"
version: "5.1.0+dfsg-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cpptraj"
---

# cpptraj(1)

fast, parallelized molecular dynamics trajectory data analysis

## 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.