[gmx-users] Chemical Potential

[Steven Neumann]

Thank you very much guys! I will search for some reading. If you can
suggest a tutorial I will appreciate.

On Thu, Jan 19, 2012 at 11:57 AM, René Pool <r.pool at vu.nl> wrote:

> Hi,
>
> If I understand the question correctly, you want to know the water
> chemical potential in the water/protein/ligand system.
> If so, in principle it should be possible to approximate the water
> chemical potential using test particle insertion. Gromacs has a utility for
> that.
>
> Cheers,
> René
>
> ==============================**=======================
> René Pool
>
> Division of Molecular and Computational Toxicology
> Department of Chemistry and Pharmaceutical Sciences
> Vrije Universiteit Amsterdam
> De Boelelaan 1083
> 1081HV AMSTERDAM, the Netherlands
> -----
> IBIVU/Bioinformatics
> Department of Computer Science
> Vrije Universiteit Amsterdam
> De Boelelaan 1081a
> 1081HV AMSTERDAM, the Netherlands
>
> Room P 2.75
> E: r.pool at vu.nl
> T: +31 20 598 76 12
> F: +31 20 598 76 10
> ==============================**=======================
>
>
>
> On 01/19/2012 02:49 PM, Ivan Gladich wrote:
>
>> On 01/19/2012 11:34 AM, Steven Neumann wrote:
>>
>>> Does anyone can help?
>>> Dear Gmx Users,
>>> I am wondering whether it is possible to obtain in Gromacs chemical
>>> potential e.g. of water in the protein - ligand system?
>>> Please, advise me to do some further reading, suggest method, maybe
>>> tutorial?
>>> Thank you,
>>> Steven
>>>
>> Dear Steven
>> I am not an expert of protein - ligand system...
>> However  the chemical potential of a i-th specie is the derivative of the
>> potential energy in function of the number of the i-particles present in
>> the system.
>> As far as I know (and if I am not wrong), in GROMACS the number of
>> particle is fixed along all the simulation, i.e., you cannot change the
>> number of particles during the simulation.
>> Therefore, you cannot simply  obtain the chemical potential from one
>> single run...
>> I suggest you to search in literature; maybe you can combine different
>> runs to obtain the chemical potential...but I do not want to say you
>> something wrong since I do not have experience in such systems.
>>
>> Good luck
>> Ivan
>>
>> --
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