Category: General Commands

parsetiming

Parse timing data from CPPTRAJ output. parsetiming … [out ] [name ] [sortby {time|cores|filename}] [includebad] [showdetails] [type {trajproc|trajread|actframe}] [reverse] [groupout [grouptype {prefix|name|kind}]] <filename args> Files containing CPPTRAJ output to get timing data from. [out <file>] Write total sorted… Read More

parallelanalysis

(MPI only) Divide current Analyses among MPI processes. parallelanalysis [sync] MPI only. Divide all currently set up analyses as evenly as possible among available MPI processes and execute. Each analysis will get a single MPI process. If sync… Read More

flatten

Distribute elements of 2d matrix across 1d array. flatten name <output set name> [mode {sum|avg}] <input set args> name <output set name> Name of flattened1D output set(s). mode {sum|avg} If sum, matrix elements will be summed. If avg,… Read More

ensextension

Enable/disable ensemble number extension for files in ensemble mode. ensextension {on|off} Turn printing of ensemble member number filename extensions on or off. By default ensemble extensions are printed in parallel and not in serial. NOTE: The ‘ensextension off’… Read More

createset

Create a dataset from a simple mathematical expression. create <filename> <datasetname0> [<datasetname1> …] [<DataFile Options>] Add specified data sets to the data file named <filename>; if the file does not exist, it will be added to the DataFileList…. Read More

calc

Evaluate the given mathematical expression. clear [{all | <type>}] (<type> = actions,trajin,trajout,ref,parm,analysis,datafile,dataset) Clear list of indicated type, or all lists if ‘all’ specified. Note that when clearing actions or analyses, associated data sets and data les are not… Read More

usediskcache

Turn caching of data sets to disk on or off. usediskcache {on|off} If on, CPPTRAJ will attempt to cache data sets to disk if possible. This currently only works for integer data sets (e.g. hbond series data sets,… Read More

sortensembledata

Sort data sets using replica information (currently constant pH only) sortensembledata <dset arg0> [<dset arg1> …] <dset arg0> [<dset arg1> …] Data set(s) to sort. Sort unsorted data sets. Currently only works for constant pH REMD data.

random

Set the default random number generator used in CPPTRAJ random [setdefault {marsaglia|stdlib|mt|pcg32|xo128}]        [createset count <#> [seed <#>]        settype {int|float01|gauss [mean ] [sd ]}] setdefault If specified, change the default random number generator… Read More