[gmx-users] Chemical Potential

[René Pool]

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

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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
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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
>