[gmx-developers] Coulomb energy calculation
Ranjit Sudhakar Ranbhor
ranjitranbhor at iitb.ac.in
Fri Jan 23 08:38:42 CET 2004
> On Fri, 2004-01-23 at 07:28, Ranjit Sudhakar Ranbhor wrote:
>> 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
>> 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
Whether I have to include 1,4 selectively?
>> 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
>> The PDB file and the calcualtions are attached.
>> Ranjit Ranbhor
>> Research Scholar
>> Biotechnology Group
>> School of Biosciences and Bioengineering
>> Powai, Mumbai 400076
> 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
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