Tools and information for AMBER and CPPTRAJ examples
Updated: March 25, 2019
Calculate eigenvectors and eigenvalues from given symmetric matrix. diagmatrix <name> [out <filename>] [thermo [outthermo <filename>]] [vecs <#>] [name <modesname>] [reduce] [nmwiz [nmwizvecs <#>] [nmwizfile <filename>]] <name> Name of symmetric matrix to diagonalize. [out <filename>] Write results to <filename>…. Read More
Posted: February 21, 2019
matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>] [name <name>] [ byatom | byres [mass] | bymask [mass] ] [ ired [order <#>] ] [ {distcovar | idea} <mask1> ] [ {dist | correl | covar |… Read More
Updated: January 26, 2024
Set up a trajectory for reading during a Run. trajin <filename> {[<start> [<stop> | last] [<offset>]]} | lastframe [parm <parmfile / tag> | parmindex <#>] [mdvel <velocities>] [mdfrc <forces>] … Read More
Updated: March 27, 2019
List various objects in the CPPTRAJ state list <type> (<type> = actions,trajin,trajout,ref,parm,analysis,datafile,dataset) List the currently loaded objects of <type>.
Updated: March 27, 2019
Run an analysis immediately or run all queued analyses runanalysis [<analysiscmd> [<analysis args>]] Run given analysis command immediately and write any data generated. If no command is given run any analysis currently set up. NOTE: When ’runanalysis’ is… Read More
Updated: April 12, 2023
Read data sets from files. readdata <filename> [name <dsname>] [as <fmt>] [separate] … Read More
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
Posted: February 20, 2019
Ranges instead of atom masks. For several commands some arguments are ranges (e.g. ’trajout onlyframes <range>’, ’nastruct resrange<range>’, ’rmsd perres range <range>’); THESE ARE NOT ATOM MASKS. They are simple number ranges using ’-’ to specify a range… Read More
Updated: January 26, 2024
The mask syntax is similar to PTRAJ. Note that the characters ’:’, ’@’, and ’*’ are reserved for masks and should not be used in output file or data set names. All masks are case-sensitive. Either names or… Read More
Updated: February 20, 2019
Cpptraj uses the AKMA system of units. The exception is time, which is typically expressed in ps (except where noted). Variable Unit Length Angstrom Energy kcal/mol Mass AMU Charge electron Time ps (typically) Force kcal/mol*Angstrom
Copyright © 2024 · All Rights Reserved · AMBER-hub
Theme: Structure Lite by Organic Themes