[gmx-users] Umbrella Sampling - Ligand Protein

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 12 12:06:13 CET 2012

Steven Neumann wrote:
> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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:
>          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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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