[gmx-users] Umbrella Sampling - spacing
s.neumann08 at gmail.com
Wed Feb 22 18:01:38 CET 2012
On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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