[gmx-users] FEP with real or dummy charges?
G.N.Patargias at leeds.ac.uk
Tue May 22 12:11:37 CEST 2007
Many thanks for your reply! Concerning the use of PME, I
also put a counter charge in bulk in order to keep the whole
So, if I understood corectly, you suggest that I should perturb
all the partial charges around the vitual site?
From: gmx-users-bounces at gromacs.org on behalf of Maik Goette
Sent: Sat 5/19/2007 12:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP with real or dummy charges?
I don't really know, if this may solve your problem, but what I want to
suggest is, not using PME for the simulation. I don't know, how other
longerange-methods behave while changing the total charge of the system,
PME won't work (as far, as I know).
Concerning your way, how to perturb the charge, it depends on, where you
think the charge sits...In general, I would assume, that a site, where a
netto charge is 0 and the same, where the netto charge is one, will be
different in partial charges of most atoms in the area. Therefore
perturbing the whole site (just the partial charges) would be the right
way to do it. This in fact means, that you have the partial charges for
the +1-charge atoms...maybe spreading the charge in a senseful way,
should do it.
Using a virtual site would be the solution for a point charge in space,
its coordinates relative to two or more atoms.
If you want to have the charge sitting on a special atom, just change
that charge explicitly, although I'm really not sure, if that's the way,
one should go.
Hope you get some help from that.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Georgios Patargias wrote:
> I want to calculate the change in free energy (electrostatic contribution only)
> when introducing a charge in a certain site of a protein using a single step
> Should this be done with charging an inserted virtual site (a dummy atom) or a
> protein atom (e.g. Ca)?
> I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am
> not sure why though...
> Thanks a lot in advance for any feedback.
> Best wishes
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
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