[AMBER] Estimation of free energy of solvation ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Wed, 15 Jun 2011 16:19:37 +0200

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,


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Received on Wed Jun 15 2011 - 08:00:05 PDT
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