CPPTRAJ:(1)

💖 CPPTRAJ:(1) — User Commands, bestie edition 💖

okay so this is the CPPTRAJ:(1) manual page, and it lives in the User Commands section. It's giving CPPTRAJ: — fast, parallelized molecular dynamics trajectory data analysis. Periodt. 💅

🎀 NAME 🎀

CPPTRAJ: — fast, parallelized molecular dynamics trajectory data analysis

✨ SYNOPSIS ✨

cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]

💅 DESCRIPTION 💅

okay so the synopsis doesn't stop there, bestie — here's the rest of the command-line lineup:

[-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}]

now the flags, one by one, no gatekeeping:

• -p <Top0> — loads <Top0> as a topology file. topology loading? slay.
• -i <Input0> — reads input from file <Input0>.
• -y <trajin> — reads from trajectory file <trajin>; same as input trajin <trajin>.
• -x <trajout> — writes 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> — reads <reference> as reference coordinates; same as input reference <reference>.
• -d <datain> — reads data in from file <datain> (readdata <datain>).
• -w <dataout> — writes data from <datain> as file <dataout> (writedata <dataout>).
• -o <output> — writes CPPTRAJ STDOUT output to file <output>.
• -h | --help — prints command line help and exits.
• -V | --version — prints version and exits.
• --defines — prints compiler defines and exits.
• -debug <#> — sets global debug level to <#>; same as input debug <#>.
• --interactive — forces interactive mode.
• --log <logfile> — records commands to <logfile> (interactive mode only). Default is cpptraj.log.
• -tl — prints length of all input trajectories specified on the command line to STDOUT.
• -ms <mask> — prints selected atom numbers to STDOUT.
• -mr <mask> — prints selected residue numbers to STDOUT.
• --mask <mask> — prints detailed atom selection to STDOUT.
• --resmask <mask> — prints detailed residue selection to STDOUT.
• --rng <type> — changes default random number generator. Types are {marsaglia|stdlib|mt|pcg32|xo128}.

⭐ * denotes flag may be specified multiple times.

okay bestie, that's the whole page. 💖 This one is CPPTRAJ: Version V5.1.0 (GitHub), from August 2022, and it's the CPPTRAJ:(1) manual. Now go analyze those trajectories, you main character. 🦋✨💅