[gmx-users] Umbrella Sampling - spacing

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 22 17:08:36 CET 2012

Steven Neumann wrote:
> Dear Gmx Users, Dear Justin,
> I run pulling of my ligand away from my protein. Then I used Justin perl 
> script to extract distances for umbrella sampling windows between my 
> ligand and crucial residue of my protein (Isoleucine). The number of 
> hydrogen bonds between ligand and protein during the pulling is app. 3 
> at the begining, then 4 in some frames and then obviously zero (when 
> ligand dissociated).
> Would you use the 1st frame as a starting window when number of hbonds 
> is 3 or further window when this is number is 4?

Assuming the first frame represents a fully-bound configuration, you should 
start there.  I'm guessing you're trying to determine the DeltaG of binding for 
your ligand.  If you define an arbitrary reaction coordinate, you get an 
arbitrary answer.  Starting and ending points dictate the value of DeltaG (since 
it is a state function).

> Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system 
> where interactions are via hydrogen bonds and hydrophobic interactions only?

Most systems interact via hydrogen bonds and hydrophobic interactions. 
Generally, 0.2 nm is a decent starting point, but should by no means be viewed 
as any sort of universal standard.  It worked for me in my tutorial, it may not 
work for others.  Consult the literature for similar systems and proceed.  If 
you find under-sampled regions along the reaction coordinate, it is trivial to 
add a new window.



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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