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
--
========================================
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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