[gmx-users] FEP with real or dummy charges?

[Georgios Patargias]

Many thanks for your reply! Concerning the use of PME, I 
also put a counter charge in bulk in order to keep the whole 
cell neutral.

So, if I understood corectly, you suggest that I should perturb
all the partial charges around the vitual site? 

George




-----Original Message-----
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.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Georgios Patargias wrote:
> Hi 
> 
> 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 
> FEP. 
> 
> 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 
> George
> 
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
> 
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