[gmx-users] Chemical Potential

René Pool r.pool at vu.nl
Thu Jan 19 12:57:34 CET 2012


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.


René Pool

Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands

Room P 2.75
E: r.pool at vu.nl
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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

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