[gmx-users] Can entropy be gained via molecular dynamics

Ran Friedman ran at hemi.tau.ac.il
Fri Mar 4 16:57:02 CET 2005


I'm not exactly sure what do you mean by "gained". If you ask whether
one can compute the entropy based on MD simulations, then the answer is
positive in principle. You can calculate the entropies of molecules from
the covariance matrix based on the quasi-harmonic approximation (J Chem
Phys 115:6289, see also my question to this list a few months ago). I
guess you should also be aware of possible complications due to
insufficient sampling in the simulations (see the publications from Berk
Hess: Phys Rev E. 62:8438, Phys Rev E. 65:31910).


zjim wrote:

> Hi everyone
> Can entropy be gained via molecular dynamics (it seems to be).
> if that do, is there any literature or example of that.
> thank you very much
> ZhouJinming
> ShanghaiInstituteofOrganicChemistry
> ComputationalChemistryLab
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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