Parameter/Reference Tagging
Parameter and reference files may be ’tagged’ (i.e. given a nickname). These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More
Tools and information for AMBER and CPPTRAJ examples
Updated: March 28, 2019
Parameter and reference files may be ’tagged’ (i.e. given a nickname). These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More
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
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
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
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
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
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