[gmx-users] umbrella sampling distances

Justin Lemkul jalemkul at vt.edu
Fri Nov 18 20:29:53 CET 2016

On 11/17/16 10:06 PM, Irem Altan wrote:
> Hi,
> 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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