[gmx-users] Free energy between residues

[Justin A. Lemkul]

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

-- 
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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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