[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 24 19:35:37 CET 2012

shahid nayeem wrote:
> My protein complex interface has a hydrophobic core and on each side of 
> this core at the edge are two hydrogen bonds. The Hydrogen bond on one 
> side is between Arg and Asp and another side it is between Arg and Glu. 
> Its experimental Kd is in nanomolar regions. How should I decide the 
> length of the simulation required in each window with this information.

As you would any other system.  Look for convergence of observables of interest. 
  Your PMF alone suggests insufficient sampling for these simulations, so as 
I've said several times, you probably need longer simulations to do so, but you 
can start by examining the physical properties of each window.  What you're 
looking for is up to you, based on your knowledge of the system at hand.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list