Steven Neumann wrote:
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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:
http://speedy.sh/y8Ssz/__profile.JPG
<http://speedy.sh/y8Ssz/profile.JPG>
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).
-Justin
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?
It's no use to blindly guess. It's up to you to assess the convergence of your
simulations and decide on an appropriate time frame.
-Justin
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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