[gmx-developers] Coulomb energy calculation

[Ranjit Sudhakar Ranbhor]

> 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.




>
>>
>>
>> >
>> >> 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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> --
> 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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