pycolvars
Python tools to post-process and analyze collective variable (CV) data from metadynamics and umbrella sampling simulations: reading colvars/PLUMED-style trajectory files, reconstructing free energy surfaces (PMF), and finding minimum energy paths across them.
This package was originally developed alongside
sea_urchin and later
split out as a standalone tool.
Installation
pip install -e .
Minimum energy path algorithm
pycolvars.min_energy_path finds the path between two basins on an energy
surface that minimises the maximum energy barrier crossed (the minimax / bottleneck
path). It uses the Minimum Spanning Tree of the grid connectivity graph (edge
weight = max endpoint energy), which provably yields the optimal minimax path.
k-th alternative paths are found by iteratively removing the bottleneck edge
of the previous best path and recomputing.
This is a native implementation using networkx. It replaces an earlier
vendored copy of MEPSAnd by
Marcos-Alcalde et al.
1 maintainer
Metadata
1 maintainer
Release files for pycolvars 0.1.0
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