gmentro.py is a program to calculate configurational entropy from a conformational ensemble using Gaussian mixtures. It is an implementation of the algorithm described in
Gergely Gyimesi, Péter Závodszky, and András Szilágyi:
Calculation of configurational entropy differences from conformational ensembles using Gaussian mixtures
J. Chem. Theory Comput., 13(1):29-41. (2017)
DOI: 10.1021/acs.jctc.6b00837 PubMed
If you use the program, please cite the above paper.
The program is written in Python (3.x recommended), and needs the
numpy module. Much of the code has been adapted from Jakob
Verbeek's Matlab code for accelerated Gaussian mixture
As a documentation, a manual page is provided in
gmentro.py.1.md, which is also available as a html
file and a regular manpage file
(copy this file into a directory in your MANPATH and you'll be able to
man gmentro.py to display the manual page).
xvg2dat.py is a helper program to create a torsion angle trajectory
file from Gromacs coordinate trajectories. See instructions in the
The Makefile only serves to create the various formats of the man page (requires the ronn program).