[gmx-developers] implicit solvent free energy

[Berk Hess]

On 08/30/2013 09:49 AM, Gerrit Groenhof wrote:
> On Aug 30, 2013, at 10:42 AM, Berk Hess wrote:
>
>> On 08/30/2013 08:52 AM, Gerrit Groenhof wrote:
>>> Hi David,
>>>
>>>
>>>>
>>>> In any case:
>>>> - Are other people similarly interested in this?
>>>
>>> Not in implementing, but having the GB code working in combination with free energy could be of interest when one wants to address the effects of periodicity and background charge on the free energy. Just not sure if tis would be worth the effort of maintaining the GB code, but I might use it.
>> You will never get around the background charge issue.
> Off topic:
>
> I thought more of comparing a GB run with periodicicty to a GB rerun without periodicity and get an estimate for the contribution of the periodicity plus background charge, without being able to disentangle these of course.
The background charge effect is inherently entangled with the 
periodicity, as it is a net charge smeared out over the whole (periodic) 
space. I think you can't learn anything from the comparison you suggest.
Also note that GB with and without periodicity is identical when the 
distance between periodic images is larger than the cut-off distance.

Cheers,

Berk
>
> Gerrit
>
>