Re: [AMBER] Estimation of free energy of solvation ?

From: Ignacio J. General <>
Date: Wed, 15 Jun 2011 10:45:30 -0400

Dear Marek:

I believe that, usually, people using MM/PBSA use very approximate
models for the entropic contribution, since it is generally not as
important as the energetic part. I won't comment on those methods
because I haven't used them. But if you are interested in using an (in
principle) exact and relatively straight forward method for entropy, I
would strongly point you in the direction of the so-called
Hypothetical Scanning Molecular Dynamics (HSMD) method. You can find
some information about it in the web page of Prof. Meirovitch,



On Wed, Jun 15, 2011 at 10:19 AM, Marek Maly <> wrote:
> Hello all,
> I am just thinking about the possibility of calculating
> free energy of solvation for the given molecule using MM/PBSA.
> Let say that I have (i) MD trajectory of the given molecule from
> simulation in vacuum and
> (ii) MD trajectory from simulation of the same molecule in explicit water.
> If I am not wrong, enthalpic contribution to the complete solvation energy
> could be estimated like:
> H(solvated molecule) - H(molecule simulated in vacuum)
> ( where H(solvated molecule) contains also interaction energy with solvent
> )
> What is not so clear to me is how to estimate the complete entropy change
> due to transfer
> of molecule from vacuum into solvent.
> Part which reflects only entropy change of solvated molecule should be
> also clear:
> T(solvated molecule) - T(molecule simulated in vacuum) which could be
> estimated using normal mode analyses
> But if I am not wrong, there is also necessary to add also entropy change
> in solvent to have entropic term complete and here I
> I would appreciate any recommendations.
> Is there any way how to estimate this contribution ? Is it eventually
> possible to say if this contribution is important
> (or comparable) with above mentioned dH or dT(solute) especially in case
> of spherical charged molecules solvated in water ?
> Thank you very much in advance for any suggestion, eventual corrections or
> links to relevant sources !
>   Best wishes,
>       Marek
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Received on Wed Jun 15 2011 - 08:00:08 PDT
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