[gmx-users] Chemical Potential

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Thu Jan 19 14:49:47 CET 2012

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 Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic

Tel: +420775504164
e-mail: ivan.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/

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