Den 2020-02-13 kl. 05:10, skrev Pathum Manjula Weerawarna:
Hi everyone,

I'm trying to estimate the configurational entropy of a small molecule using 
gmx anaeig. However, it does not allow me to use a mass-weighted covariance 
matrix for the calculation (only allow me to use mass-unweighted CV matrix). 
Theoretically, the use of a mass unweighted CV matrix for entropy calculation 
is inaccurate (frequencies going to be smaller). Does anybody know the accuracy 
of the entropy calculated using gmx anaeig? Also, is there any way to use a 
mass-weighted CV matrix for this calculation?

The entropy is only the conformational entropy and can therefore be used for determining relative entropies, for instance for ligand binding (J Chem Theory Comput 9 pp. 4542-4551 (2013)). If you want to compute absolute entropies then for now normal mode analysis is the most efficient, even though it has limitations as well. See J Phys Chem A. 122 pp. 8982-8988 (2018).

Sorry to promote my own papers but this is what I know :)

Thank you so much for the help


Pathum M. Weerawarna, Ph.D.
Postdoctoral Fellow
Silverman Research Group
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston, IL 60208-3113

Phone: (316) 990-8542
Email :

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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