[gmx-users] Free energy between residues
s.neumann08 at gmail.com
Thu Jun 28 12:51:49 CEST 2012
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
>> and then g_dist.
> If you are using PME, there is no trivial way to decompose the reciprocal
> space term.
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
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