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

[Miguel Caro]

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?

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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>

-- 
*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