[gmx-developers] Coulomb energy calculation

[Ranjit Sudhakar Ranbhor]

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.

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
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