[gmx-users] Charge calculation in Gromacs

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 7 15:27:02 CEST 2006

> Dear All who may concern,
>     I have some questions for the charge calculation in Gromacs, I used
> the
> forcefied ffG43a1 for the protein and inhibitors. Does the charge for the
> protein is the charge  per residue?

The charge on a residue is the sum of the charges on the (united) atoms
that make it up. The charge on a protein is the sum of the charges on the
residues that make it up (or all of the atoms, obviously). The charge per
residue is almost never considered, as it normally doesn't aid anybody
understanding physical behaviour. Hope that answers your question, because
I can't understand it.

> This forcefield is just for the polar
> H,
> right? For the nonpolar H, it will merge the H into the Heavy atom, right?

Don't know in this specific case, but there are such forcefields.

> I
> would like to know that does this force field also calculate the charge
> for
> the nonpolar H and then sum the charge with the heavy atom which it
> connects
> to or it doesn't calculate the charge for the nonpolar H?

The charge on a united atom is just a number - as is the charge on a polar
H, or any H in a non-united-atom force field. You can think of it as the
sum of the charges on the multiple atoms it models if it helps.

> Does the charge
> of
> the Heavy atom is its own charge without sum together with the nonpolar H
> which connect to it? Moreover, I would like to know that if I would like
> to
> use quantum mechanics (qm)  to calculate the charge for my inhibitor, what
> should be the method and the basis set to use to calculate for the charge
> to
> make it compiles with the ffG43a1 force fields?

Sounds like you should find the documentation (journal article?) for this
force field and read it. Also some introductory material on how force
fields work sounds like it might be worthwhile :-) Wanting to extend a
force field you don't understand yet is a recipe for disaster...


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