[gmx-users] PMF of a single water molecule respect to a surface

Justin Lemkul jalemkul at vt.edu
Sat Feb 13 06:15:50 CET 2016

On 2/12/16 8:47 AM, Alexander Alexander wrote:
> Dear Gromacs user,
> I am calculation the PMF of a single water molecule to pull it away from
> top of metallic surface along vacuum in the Z direction ,following the
> Justin umbrella tutorial. I am only  interested in the behavior of PMF in
> 0.002 nm to 0.8 nm intervalon top of the surface, but I do not why the
> population of the generated frames in this interval is really low and then
> the result is so poor.
> So, would you please let me know which parameter I should play around with?
> I just tried 0.001 instead 0.01 as the "pull_coord1_rate" and simultaneously
> 3500 instead of 1000 as "pull_coord1_k", but the result got even worse.

How often are you saving the snapshots?  I presume you're referring to the 
generation of initial coordinates as references for the individual windows. If 
you don't save frequently enough, you may miss one that you need, although it 
should be pretty easy to capture something "close enough" to start.

Your biggest problem is the very short distance you're considering here.  0.002 
nm?  You're going to have massive repulsion at that distance, such that you're 
not likely to observe any stable configurations there.  Probably anything less 
than 0.1 or 0.2 nm is going to be pretty unstable, depending on the nature of 
the interactions.



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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