[gmx-users] Charges for Coulomb potential

[Mark Abraham]

On 08/29/2012 11:08 PM, Delmotte, Antoine wrote:
> Dear Gromacs users,
>
> I would like to know which charges are used by Gromacs in the 
> calculation of electrostatic interactions in the standard coulomb 
> potential:
>
> E_electrostatics = 138.935 * q1 * q2 / (epsilon_r  * r_12);
>
> Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the 
> force field used?

If you use pdb2gmx to generate your .top, yes. More generally, GROMACS 
uses the charges found in the .top.

> Could you also please redirect me towards the relevant literature for 
> the calculation of epsilon_r in Gromacs?  (or does Gromacs uses a 
> fixed epsilon_r?)

You choose it. See parts of manual 4.1 and 7.3

Mark