Steven Neumann wrote:
On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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>
<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>
<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
Thank you Justin. Is there any way to find out after deltaG the entropic
contribution to binding free energy?
Probably, but having never done it I can't offer any specific guidance. Perhaps
others on the list can. I would certainly suggest you seek a protocol in the
literature; I feel sure that I've seen such endeavors.
-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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