Adds new commands to cpptraj: one for performing time-independent correlation analysis (TICA), one for calculating the minimum distance between atoms or pairs of residues/molecules, one for calculating the maximum distance, and one for projecting 1D data sets along eigenmodes.
New analysis command: tica
{ crdset <COORDS set name> [mask <mask>] |
data <input set arg1> ... }
[lag <time lag>] [map {kinetic|commute|none}]
[name <output set name>] [out <file>] [cumvarout <file>]
This is a useful (often faster) alternative to project for 1D data sets when you don't have to project coordinates. The projection command has also been updated to allow projection of regular 1D data sets (on e.g. TICA modes). The matrix command will be updated to allow covariance calculation on 1D data sets in another PR.
Version 6.24.1.
Adds new commands to cpptraj: one for performing time-independent correlation analysis (TICA), one for calculating the minimum distance between atoms or pairs of residues/molecules, one for calculating the maximum distance, and one for projecting 1D data sets along eigenmodes.
New analysis command:
ticaNew actions:
mindist/maxdistNew analysis command:
projectdataThis is a useful (often faster) alternative to
projectfor 1D data sets when you don't have to project coordinates. Theprojectioncommand has also been updated to allow projection of regular 1D data sets (on e.g. TICA modes). Thematrixcommand will be updated to allow covariance calculation on 1D data sets in another PR.Adds tests and updates the manual.