[gmx-users] Umbrella Sampling - Ligand Protein
s.neumann08 at gmail.com
Mon Mar 12 11:53:55 CET 2012
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Steven Neumann wrote:
>> Hi Justin,
>> As you advised I reduced number of my windows and I obtined histogram:
>> http://speedy.sh/2b9dT/histo.**JPG <http://speedy.sh/2b9dT/histo.JPG>
>> Which looks really good.
>> The corresponding profile:
>> I do not understand it. Does my deltaG of binding correspond to
>> everything above 0 kcal/mol which is 6 kcal/mol?
> DeltaG = the free energy difference between the final and initial states.
> So that's up to you to decide. Your curve is rather rough and the energy
> minimum potentially still ill-defined. The histograms indicate that the
> sampling overlap is likely fine, you just may need a bit more sampling in
> each window to smooth things out. Also make use of the error estimates
> that g_wham can provide; they can be quite informative (and necessary).
Thank you Justin. In each window I run the simulation of 10 ns. Do you
think that making it 20 ns will make the profile more smooth?
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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