On 6/28/12 6:51 AM, Steven Neumann wrote:
On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul <jalem...@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.ri...@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
--
========================================
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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