[gmx-users] workaround for PME coulomb energy (fwd)

[David]

On Tue, 2002-11-26 at 17:40, David L. Bostick wrote:
> 
> 
> Hello David,
> 
> Thanks for your help with the workaround.  I have an additional question
> pertaining to your last reply below:
> 
> > E(lr) = E(lr) (ion-ion) + E(lr) (ion-rest) + E(lr) (rest-rest)
> > Setting the ion charge to zero will give you E(lr) (rest-rest)
> > setting the rest to zero will give you E(lr) (ion-ion)
> > but if you have only one ion that term will be zero. Do check the charge
> > correction to PME, as that may be different when the total charge
> > changes.
> 
> How do I check the charge correction to PME?
Good question, you'll probably have to look at the equations. (Didn't
you fid a bug in them at some stage?) The correction is included in the
PME energy, but if you have two systems with a net charge it may be
tricky... 

> 
> Thanks,
> David
> 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> David Bostick					Office: 262 Venable Hall
> Dept. of Physics and Astronomy			Phone:  (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall				dbostick at physics.unc.edu
> Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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> 
> On 23 Oct 2002, David wrote:
> 
> > On Wed, 2002-10-23 at 17:44, David L. Bostick wrote:
> > >
> > > Hello all,
> > >
> > > I am interested in using David van der Spoel's method for calculating the
> > > total coulomb energy of a single ion with the rest of the system.  I just
> > > want to ask a few questions so I can feel comfortable with what I'm doing.
> > >
> > > 1)If I take the original .edr file from the simulation, is the total
> > > coulomb energy of the system Coulomb (SR) + Coulomb (LR) as extracted by
> > > g_energy?  That is.. Coulomb 1-4 doesn't really factor in does it?
> > In this case it is constant, yes.
> >
> > >
> > > 2)Then if I set the ion charge to zero and rerun to generate a new .edr
> > > file and calculate the total coulomb energy again as Coulomb (SR) + Coulomb
> > > (LR), this will be the total PME energy for System_&_!ion-System_&_!ion?
> > Coulomb (SR) you can do in groups anyway, so you can get that more
> > accurate from the original run.
> >
> > > 3)Then I can subtract the result of #2 from the result of #1 and obtain the
> > > total coulomb PME energy of System_&_!ion-ion?  Since there is only one
> > > ion, the coulomb energy of ion-ion is zero so I don't have to worry about
> > > it.
> > E(lr) = E(lr) (ion-ion) + E(lr) (ion-rest) + E(lr) (rest-rest)
> > Setting the ion charge to zero will give you E(lr) (rest-rest)
> > setting the rest to zero will give you E(lr) (ion-ion)
> > but if you have only one ion that term will be zero. Do check the charge
> > correction to PME, as that may be different when the total charge
> > changes.
> >
> > > 4)If I write the total ewald sum in the traditional way,
> > >
> > >       E = E(real) + E(reciprocal) + E(self) + E(dipole_correction)
> > >
> > >   is the coulomb energy as extracted by g_energy as follows:
> > >
> > >    Coulomb (SR) = E(real)
> > >
> > >   and
> > >
> > >    Coulomb (LR) = E(reciprocal) + E(self) + E(dipole_correction) ?
> > >
> > >    How exactly are these terms divided among the two quantities Coulomb(SR)
> > >    and Coulomb(LR)?
> > Coulomb(LR) = E(reciprocal) + E(self) + E(dipole_correction)
> > Coulomb(SR) = E(real)
> >
> >
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> > Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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