[gmx-users] Charges for Coulomb potential

[Delmotte, Antoine]

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?

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?

Thank you,

Antoine

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 
>> 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