[gmx-users] Entropy calculations for simple systems (water)

michal.kolar at marge.uochb.cas.cz michal.kolar at marge.uochb.cas.cz
Fri Sep 4 16:14:43 CEST 2015

Dear Miguel,
it appears that the water dynamics is far from being harmonic thus the
analysis of the covariance matrix would be useless. You may wish to check
the following paper:

Reinhard F, Grubmüller H. Estimation of absolute solvent and solvation
shell entropies via permutation reduction. J. Chem. Phys. 126, 014102

with best


> Dear all,
> I'm trying to perform entropy calculations with GROMACS. To get started
> I'm trying to get the entropy of water using the TIP4P and TIP3P models.
> At the moment I'm running a MD simulation of different size boxes for
> around 1ns and using the following analysis tools:
>     g_covar_d -f md.xtc -s md.tpr -b 100 -v eigenvec.ttr
>     g_anaeig_d -v eigenvec.trr -entropy -temp 298
> I get the following result for a sample calculation with 57 TIP3P water
> molecules (I get similar results for the TIP4P model, and approx.
> linearly increasing entropy with box size):
>     The Entropy due to the Quasi Harmonic approximation is 7567.68 J/mol K
>     The Entropy due to the Schlitter formula is 7677.06 J/mol K
> I have several questions:
>  1. Are the commands I'm using a sound approach?
>  2. I am assuming that I should divide the entropy value by the number
>     of molecules to get the actual result, when I do so for the above I
>     get 133 J/mol K (QH approximation) which is about twice as large as
>     the experimental value (about 70 J/mol K).
>  3. Should I expect this kind of large disagreement? Is it due to the
>     approximation used to calculate the entropy? I have checked results
>     from JPC B 114, 8195 (2010) where the 2PT model obtains entropy
>     values in good agreement with experiment for both TIP4P and TIP3P
>     water models.
>  4. What could be triggering this error in my simulation results? Am I
>     doing something obviously wrong?
> Many thanks,
> Miguel
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcaroba at gmail.com*
> Work: *miguel.caro at aalto.fi*
> Website: http://mcaroba.dyndns.org
> --
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