Dear Ignacio,
thanks a lot for this hint !
Best wishes,
Marek
Dne Wed, 15 Jun 2011 16:45:30 +0200 Ignacio J. General
<ijgeneral.gmail.com> napsal/-a:
> 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,
> http://www.ccbb.pitt.edu/Faculty/meirovitch/index.htm.
>
> Regards,
>
> Ignacio
>
> On Wed, Jun 15, 2011 at 10:19 AM, Marek Maly <marek.maly.ujep.cz> 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 - 08:30:03 PDT
