Category: Running CPPTRAJ

Trajectory Processing “Run”

Updated: November 4, 2021

Like ptraj, a trajectory processing “Run” is one of the main ways to run cpptraj. First the Run is set up via commands read in from an input file or the interactive prompt. Trajectories are then read… Read More

Category: CPPTRAJ, Running CPPTRAJ

Interactive mode

Posted: February 20, 2019

In “interactive mode” users can enter commands in a UNIX-like shell. Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses. If cpptraj is run with ’–interactive’, no arguments, or… Read More

Category: CPPTRAJ, Running CPPTRAJ

Tags: running cpptraj

Batch mode

Posted: February 20, 2019

In “batch” mode, cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN. The syntax of <input file> is similar to that of ptraj. Keywords specifying different commands… Read More

Category: CPPTRAJ, Running CPPTRAJ

Tags: running cpptraj

Commands

Updated: November 4, 2021

Input to CPPTRAJ is in the form of commands, which can be categorized in to 2 types: immediate and queued. Immediate commands are executed as soon as they are encountered. Queued commands are initialized when they are… Read More

Category: CPPTRAJ, Running CPPTRAJ

Tags: running cpptraj

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