[gmx-users] Charges for Coulomb potential

[Delmotte, Antoine]

Alright, I understand now.

Many thanks for this!

Antoine

Le 29/08/2012 18:57, Mark Abraham a écrit :
> 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 
> at once.
>
>>
>> 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).
>
> Mark
>
>>
>> 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
>>
>