[gmx-users] RE: Neutralising charge distribution

[David van der Spoel]

Georgios Patargias wrote:
> Hi Jeroen
> 
> Thank you for your reply. I just wanted to know whether the correction 
> term for the 'uniform background charge' is included in the code;  I didn't 
> meant to to take it out.
> 
> Another thing is about the dipole correction that is applied for conducting 
> boundary conditions. Is it switched off in PME when epsilon-surface is 0?
> 
check the equations in the manual, they are correct (famous last words...)

> Regards 
> George
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of van Bemmelen
> Sent: Tue 9/18/2007 11:14 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] RE: Neutralising charge distribution
>  
> Hi George,
> 
> Yes, such a correction term exists, but it's a divergent term. This term
> is IMPLICITLY included in the energy, since it compensates for the
> divergent part in the reciprocal space term, leaving a constant term.
> This constant term is included explicitly in the code.
> 
> You could take this constant term out. But be very aware that this
> constant term not only represents the 'uniform background charge' (or
> 'neutralising charge distribution', if you will) but also the divergent
> part of reciprocal space term. So simply leaving it out would be highly
> unphysical, at least in my opinion.
> 
> If you really want to know more, I suggest digging into the formulas
> yourself. :-)
> 
> Greetz,
> Jeroen
> 
> 
>> Date: Mon, 17 Sep 2007 16:17:17 +0100
>> From: "Georgios Patargias" <G.N.Patargias at leeds.ac.uk>
>> Subject: [gmx-users] Neutralising charge distribution
>> To: <gmx-users at gromacs.org>
>> Message-ID:
>> 	<468DD857FE1E044DAE50E1D62FB57E70155D34 at HERMES4.ds.leeds.ac.uk>
>> Content-Type: text/plain;	charset="iso-8859-1"
>>
>> Hello 
>>
>> I would like to ask what is the functional form of the uniform 
>> neutralising charge distribution applied in Gromacs when doing 
>> PME on a charged system. 
>>
>> Is there a correction term for this charge distribution that 
>> is included in the calculation of energies?
>>
>> Thanks
>> George
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se