cpptraj1
Fast, parallelized molecular dynamics trajectory data analysis
Usage
cpptraj [-p
<Top0>]
[-i
<Input0>]
[-y
<trajin>]
[-x
<trajout>]
Overview
-
[-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.