[gmx-users] Free energy between residues

[Steven Neumann]

On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/28/12 6:33 AM, Steven Neumann wrote:
>>
>> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
>>>
>>> Dear Steven,
>>>
>>> Where are you working?
>>
>>
>> I work in UK, London. Why are you asking?
>>
>>
>>> >From my experience the g_energy  -fee only gives a free enrgy estimate
>>> for the whole system, so one has to pull out all the energy terms based on
>>> your index file of interest and sum them in a spread sheet.  if the -fee can
>>> do the energy estimates for a specific set, please let me know this would be
>>> valuable to me.
>>
>>
>> I think I will just need a potential energy between those residues (LR
>> and Coulombic) and then can get the effective potential
>> Ueff=-kTln<e(-BU)
>> and then g_dist.
>>
>
> If you are using PME, there is no trivial way to decompose the reciprocal
> space term.
>
> -Justin

But if I will get the effective potential with respect to the distance
I can adjust non bonded parameters to this curve in coarse grained
model. Am I right?

>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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