[gmx-users] Calculation of configurational entropy

David van der Spoel spoel at xray.bmc.uu.se
Sun Apr 2 17:10:36 CEST 2017

On 02/04/17 14:20, Saumyak Mukherjee wrote:
> Dear Users,
> I want to calculate the configurational entropy of certain water molecules
> in a protein water system. Can you kindly inform me how to do it?
Basically it is not meaningful since first most water molecules are 
rigid in simulation, meaning there is only translational and rotational 
entropy, and second they will diffuse and be replace by others.
>>From different forums I have seen that it can be down by using g_covar and
> g_anaeig programs. But I don't clearly understand the use. From this I am
> getting just a single entropy value. How an I get the entropy as a function
> of time?
There is no such thing.

In theory you can compute entropy over parts of a trajectory and print 
it as a function of time for each block, but those blocks need to be 
long to be meaningful.
> Thanks in advance,
> Saumyak

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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