[gmx-developers] Coulomb energy calculation

[David van der Spoel]

On Fri, 2004-01-23 at 11:06, Ranjit Sudhakar Ranbhor wrote:
> > 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 calculating the Coulomb (SR ie 1,5 onwards) for the following pairs
> 
> Atom (atom no.)
> 
> C(2) with O(9), N(10), H(11)
> O(3) with C(8), O(9), N(10), H(11)
> N(4) with H(11)
> H(5) with O(9), N(10), H(11)
> C(8) with O(3)
> O(9) with C(2), O(3), H(5)
> N(10) with C(2), O(3), H(5)
> H(11) with C(2), O(3), N(4), H(5).
> 
> In topology file nrexcl was set to 3.

That seems consistent then. Do you compare to the gromacs energy after
minimization or on step 0? (should be the latter!)
> 
> 
> 
> 
> >
> >>
> >>
> >> >
> >> >> 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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> >
> 
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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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