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

[Georgios Patargias]

Thanks again for the reply. A virtual point charge 
is what I want. 

Best wishes 
George



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Maik Goette
Sent: Wed 5/23/2007 12:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP with real or dummy charges?
 
No.
I said, you may want to perturb all partial charges in the site, where 
the netto +1 charge sits OR place a virtual site somewhere in between, 
to grow a point charge, whereas I'm not sure, if a point charge is, what 
you want.

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:
> 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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