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
=====================================================
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.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
