[gmx-developers] Coulomb energy calculation

[David]

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.

> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++