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calculate configurational entropy from a conformational ensemble
Python HTML Roff Makefile
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CITATION.txt
LICENSE.txt
Makefile
README.md
gmentro.py
gmentro.py.1
gmentro.py.1.html
gmentro.py.1.md
gmentro.py.man.ronn
xvg2dat.py

README.md

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 learning.

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 use 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 program file.

The Makefile only serves to create the various formats of the man page (requires the ronn program).

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