[gmx-users] Umbrella sampling: window distance - harmonic force constant
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
> 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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