[gmx-users] Chemical Potential
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
> Thank you,
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
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.
Ivan Gladich, Ph.D.
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
e-mail: ivan.gladich at uochb.cas.cz
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