[gmx-users] Entropy calculations for simple systems (water)
David van der Spoel
spoel at xray.bmc.uu.se
Sun Sep 6 10:20:03 CEST 2015
On 04/09/15 16:36, Miguel Caro wrote:
> Dear Michal,
>
> Many thanks for your reply. Since I have never performed this kind of
> calculation before I was actually worried that I am doing something
> wrong. Then, according to you, a poor description of the entropy of
> water is to be expected from the quasi-harmonic approximation even if
> the force field used (e.g. TIP4P) gives a reasonably good description -
> am I getting this right?
Another way is
Lin, S.-T.; Maiti, P. K.; Goddard III, W. A. J. Phys. Chem. B 2010, 114,
8191–8198.
This is implemented in a development version of gmx dos.
>
> Thanks also for the reference, I will have a look.
>
> All the best,
> Miguel
>
> On 2015-09-04 17:08, michal.kolar at marge.uochb.cas.cz wrote:
>> 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
>> (2007)
>>
>> with best
>>
>> michal
>>
>>
>>
>>> 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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>>
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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