[gmx-users] Free energy between residues

[Justin A. Lemkul]

On 6/28/12 6:51 AM, Steven Neumann wrote:
> 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?
>

Honestly, I have no idea on what intend to adjust.  Certainly you can tweak 
things in any way you like, but that doesn't mean the answer makes sense or that 
what you've done is justifiable.  To me, umbrella sampling seems far more 
straightforward.

-Justin

-- 
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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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