CPPTRAJ: - fast, parallelized molecular dynamics trajectory data
analysis
cpptraj [-p <Top0>] [-i <Input0>]
[-y <trajin>] [-x <trajout>]
- [-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.