[gmx-users] umbrella sampling distances
jalemkul at vt.edu
Fri Nov 18 20:29:53 CET 2016
On 11/17/16 10:06 PM, Irem Altan wrote:
> I’m trying to apply umbrella sampling to a system following Justin Lemkul’s tutorial. I’m confused about how the distances are calculated, however. When I run a pull simulation and calculate center of mass distances with gmx distance, I see that the distance in the 0th configuration is 3.003 nm. When I look at the output PMF generated with gmx wham, the PMF starts from 2.56 nm. What could I be missing?
Your sampling includes distances as low as 2.56 nm. This isn't necessarily
wrong. The average in the window should match the average calculated by gmx
distance, but without seeing a whole lot of steps that you left out in your
description, it's impossible to know if your setup is exactly what you think it
is. Confirm the reference distance that grompp prints out before the run,
consider the strength of the spring constant for the restraint, etc.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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