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
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