gmx_clusterByFeatures
It can be used to cluster the conformations of a molecule in a molecular dynamics trajectory using collection of features. The features could be any quantity as a function of time such as Projections of eigenvector from PCA or dihedral-PCA, distances, angles, channel radius etc.
See details at: gmx_clusterByFeatures homepage
Note
It is developed for GROMACS MD trajectory. However, it can be used with any other trajectory format after converting it to GROMACS format trajectory.
Installation on Linux and MacOS
sudo pip3 install gmx-clusterByFeaturesNo dependency on GROMACS. Install and use it.
For more details, visit download and installation section.
Usage
| Command | Function |
|---|---|
| cluster | Main module to perform clustering |
| featuresplot | Feature vs Feature plot to check quality of clustering |
| distmat | Distance-matrix related calculations |
| matplot | To visulaize/plot matrix obtained from distmat
|
| hole | To calculate cavity/channel radius using HOLE program |
| holeplot | To calculate average and plot hole output radius file |
| holefeatures | To write radius as a features for clustering |
| holeclustersplot | To plot or write radius for clusters separately |
For more details, visit usage section.
