[gmx-developers] Coulomb energy calculation

[David van der Spoel]

On Fri, 2004-01-23 at 08:38, Ranjit Sudhakar Ranbhor wrote:
> > On Fri, 2004-01-23 at 07:28, Ranjit Sudhakar Ranbhor wrote:
> >> Hi,
> >>
> >> I am calculating Coulomb energy of Ace-ALA-NHMe dipeptide unit but the
> >> values are not matching with Gromacs values.
> >>
> >> I did the energy minimisation of dipeptide to bring it in the Gromacs
> >> standard parameters of bond lengths and bond angles. After that I am
> >> calcuating the distances between the charge pairs in nm. Also I have
> >> considered the charge group concept. I am calculating Coulomb (SR) ie I
> >> am
> >> excluding 1,4 and also 1,5 if 1,4 and 1,5 are in the same charge group.
> >
> >
> > Gromacs does not exclude 1-5, not even in the same charge group.
> 
> If I do so, energy goes up to -251.0775 kJ/mol and by Gromacs it is
> -153.621 kJ/mol.
> 
> Whether I have to include 1,4 selectively?
We usually omit 1-4 interactions where one of the atoms is a hydrogen.
Otherwise the Coulomb interaction are taken into account fully. Do you
have a list of pairs, or did you set nrexcl to 2?
(but not both...)

> 
> 
> >
> >> I am using the following formula
> >>
> >> E = (138.935485 Qi * Qj) / Rij
> >>
> >> where Qi and Qj are in esu
> >> Rij in nm.
> >>
> >> The energy minimised file is giving energy -153.621 kJ/mol by Gromacs
> >> (GROMOS ffG43a1 force field) and the calculated values is coming
> >> -22.0135
> >> kJ/mol.
> >>
> >> The PDB file and the calcualtions are attached.
> >>
> >> Regards,
> >>
> >> Ranjit Ranbhor
> >> Research Scholar
> >> Biotechnology Group
> >> School of Biosciences and Bioengineering
> >> Powai, Mumbai 400076
> >> India
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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