Category: CPPTRAJ

Command Line Syntax

Updated: August 30, 2023

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>]… Read More

Category: Action Commands, CPPTRAJ

Tags: analysis

Data Set Math

Updated: November 18, 2023

Operations with data sets As of version 15, CPPTRAJ can perform basic math operations, even on data sets (with some limitations). Currently recognized operations are: Operation Symbol Minus – Plus + Divide / Multiply * Power ^ Negate… Read More

Category: CPPTRAJ, Data Sets and Data Files

Tags: data files, data sets

hbond

Updated: April 12, 2023

Calculate hydrogen bonds using geometric criteria. hbond [<dsname>] [out <filename>] [<mask>] [angle <acut>] [dist <dcut>] [donormask <dmask> [donorhmask <dhmask>]] [acceptormask… Read More

Category: Action Commands, CPPTRAJ

Tags: analysis, hbond

Parallelization

Updated: October 4, 2022

CPPTRAJ has many levels of parallelization. These levels can be enabled via the ’-mpi’, ’-openmp’, and/or ’-cuda’ configure flags for MPI, OpenMP, and CUDA parallelization respectively. At the highest level, trajectory and ensemble reads are parallelized with MPI…. Read More

Category: CPPTRAJ, Running CPPTRAJ

Tags: running cpptraj