[gmx-users] On computing entropies using g_anaeig

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 27 00:24:54 CEST 2011

Hari Shankar M wrote:
> Gmx-users,
> There has been a earlier post on differences in entropies computed using 
> the covariance analysis and normal mode analysis 
> (http://lists.gromacs.org/pipermail/gmx-users/2009-April/041535.html). I 
> discovered the reason for the differences and thought that this 
> information might be useful to others.
> 1. g_anaeig tool used to compute the entropy, computes entropies from 
> the eigenvalues of the covariance matrix only. So, feeding the 
> eigenvalues obtained from the mass-weighted Hessian to g_anaeig gives 
> meaningless entropy values. Probably, this information should be clearly 
> stated in the manual to prevent any potential abuse of g_anaeig. I 
> compared the results on a diatomic molecule (oxygen) and benzene, and 
> found very different results. The values differ by an order of 
> magnitude. Also, looking at the source code of gmx_anaeig.c, it is clear 
> that the entropies are computed from the covariance eigenvalues and not 
> the eigenvalues of the Hessian.

I have created a new bug report on the redmine site for this issue.  If you have 
a code patch or any additional information to contribute, please do so:


> 2. There is a user-developed code distributed on the gromacs website 
> called 'calc_entropies.pl'. This script can be used to compute entropies 
> from eigenvalues obtained by covariance analysis or normal mode 
> analysis. However, there seems to be a bug in this code. While the 
> conversion of the eigenvalues to eigenfrequencies is done correctly in 
> this code, there is a huge difference in the formula used to compute the 
> entropy in the case of normal modes (for entropy formula refer to 
> Karplus and Kushik 1981 paper). After correcting the entropy formula, I 
> was able to get similar results with either method. If you are 
> interested in the corrected script, you could email me at hari711 at yahoo.com.

This would make a nice contribution to the Gromacs website.  Please consider 
uploading it to the User Contributions page with a suitable description.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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