Category: CPPTRAJ

Command Line Syntax

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

hbond

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

Parallelization

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