[gmx-developers] Coulomb energy calculation

[David van der Spoel]

On Fri, 2004-01-23 at 11:38, Ranjit Sudhakar Ranbhor wrote:
> > 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 comparing the energy with the last step from the log file generated.
> 
> Is it possible otherwise to make use of Gromacs source code to calculate
> energy values (coulomb SR) of the PDB files without energy minimising them
> (all PDBs generated with standard Gromacs bond length and bond angle
> parameters)? Which program should I use to get Coulomb SR calculations?
> 
Just set nsteps to 0 or 1. And run minimization.

> 
> >>
> >>
> >>
> >>
> >> >
> >> >>
> >> >>
> >> >> >
> >> >> >> 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
> >> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> >
> >> >> > _______________________________________________
> >> >> > gmx-developers mailing list
> >> >> > gmx-developers at gromacs.org
> >> >> > http://www.gromacs.org/mailman/listinfo/gmx-developers
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> >> >> >
> >> >>
> >> >> _______________________________________________
> >> >> gmx-developers mailing list
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> >> >> www interface or send it to gmx-developers-request at gromacs.org.
> >> > --
> >> > 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
> >> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >
> >> > _______________________________________________
> >> > gmx-developers mailing list
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> >> >
> >>
> >> _______________________________________________
> >> gmx-developers mailing list
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> >> http://www.gromacs.org/mailman/listinfo/gmx-developers
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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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
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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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