[gmx-users] Charges for Coulomb potential
Mark.Abraham at anu.edu.au
Wed Aug 29 19:57:12 CEST 2012
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
> Many thanks for your quick response, Mark.
> So epsilon_r is actually different from the actual relative
> permittivity (which would be like 80 for water), is that right?
You can have an atomistic solvent or a continuum solvent, but not both
> If so, how does one usually chooses this value of epsilon_r? Is the
> default value of 1 applicable for most cases (like for simulations in
> water), or should one obtain it from the literature somehow?
The force field defines it (normally to 1).
> Thank you,
> On 29/08/12 14:47, Mark Abraham wrote:
>> 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
>>> 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
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