Category: CPPTRAJ

parallelanalysis

Posted: April 6, 2022

(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

Category: CPPTRAJ, General Commands

flatten

Updated: April 6, 2022

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

Category: CPPTRAJ, General Commands

ensextension

Updated: April 6, 2022

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

Category: CPPTRAJ, General Commands

createset

Updated: July 11, 2022

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

Category: CPPTRAJ, General Commands

calc

Posted: April 6, 2022

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

Category: CPPTRAJ, General Commands

silenceactions

Posted: April 6, 2022

Prevent Actions from writing in format information to STDOUT.

Category: CPPTRAJ, General Commands

usediskcache

Updated: April 6, 2022

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

Category: CPPTRAJ, General Commands

sortensembledata

Updated: April 6, 2022

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.

Category: CPPTRAJ, General Commands

readensembledata

Updated: May 31, 2022

Read data files in ensemble mode. readensembledata <filename> [filenames <additional files>] [<readdata args>] <lename> Lowest replica file name. filenames <additional files> Specified additional members of the ensemble. If not specified ensemble members will be search for using numerical… Read More

Category: CPPTRAJ, Trajectory File Commands

cphstats

Updated: April 6, 2022

Calculate statistics for constant pH data sets. cphstats <pH sets> [name <name>] [statsout <statsfile>] [deprot] [fracplot [fracplotout <file>]] <pH sets> Previously read in pH data sets. name <name> Output set name. statsout <statsle> Write pH statistics to <statsfile>… Read More

Category: Analysis Commands, CPPTRAJ