[gmx-users] Umbrella sampling: window distance - harmonic force constant

Justin Lemkul jalemkul at vt.edu
Tue Mar 27 21:12:49 CEST 2018

On 3/27/18 4:44 AM, Hermann, Johannes wrote:
> Dear All, dear Justin,
> I am playing around with my umbrella sampling setup and I was looking 
> at your paper which you linked in your umbrella sampling tutorial 
> ("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using 
> Molecular Dynamics").
> Up to a distance of 2nm you use a 0.1nm spacing, beyond a 0.2nm 
> spacing. Which harmonic force constant pull_coord1_k do you use for 
> the 0.1nm spacing? In comparison to the 0.2nm spacing, where 
> pull_coord1_k=1000.
> Is there a general rule of thumb between window distance and force 
> constant? Or is it always try and error while checking the histograms?

You can set the value of k based on experimental methods or somewhat ad 
hoc, but then yes, you have to check overlap. I don't know of any useful 
way of trying to predict how the intermolecular forces in the system 
will respond in such a way that you can exactly say a priori how to set 
up the windows.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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