Category: CPPTRAJ

time

Updated: April 10, 2022

Add/remove/modify time information in frames. time {time0 <initial time> dt <step> [update] | remove} time0 <initial time> Time of the first frame (ps). dt <step> Time step between frames (ps). [update] If specified, modify any existing time info…. Read More

Category: Action Commands, CPPTRAJ

xtalsymm

Updated: April 10, 2022

Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume. xtalsymm <mask> group <space group> [collect [centroid]] [ first | reference | ref <name> | refindex <#> ] [na <na>] [nb <nb>] [nc <nc>] <mask>… Read More

Category: Action Commands, CPPTRAJ

fiximagedbonds

Posted: April 10, 2022

Fix bonds which have been split across periodic boundaries by imaging. fiximagedbonds [<mask>] <mask> Mask expression of atoms to check. Fix bonds that have been split across periodic boundary conditions by imaging. It may be desirable to reimage… Read More

Category: Action Commands, CPPTRAJ

dihrms

Updated: April 10, 2022

Category: Action Commands, CPPTRAJ

keep

Updated: November 11, 2023

Keep specified atoms in system. keep [ bridgedata <bridge data set> [nbridge <#>] [nobridgewarn] [bridgeresname <res name>] bridgeresonly <resrange>] ] [keepmask <atoms to keep>] [charge <new charge>] … Read More

Category: Action Commands, CPPTRAJ

align

Updated: September 23, 2023

Align structure to a reference. align <mask> [<refmask>] [move <mask>] [mass] [ first | reference | ref <name> | refindex… Read More

Category: Action Commands, 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