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
--
------
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.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
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