[gmx-users] error with cut-off length using verlet scheme in stochastic dynamics simulation

Justin Lemkul jalemkul at vt.edu
Wed Sep 28 21:15:54 CEST 2016

On 9/28/16 3:12 PM, Amanda Parker wrote:
> Hello,
> I am trying to run a stochastic dynamics simulation and am getting the
> error:
> "The cut-off length is longer than half the shortest box vector or
>   longer than the smallest box diagonal element. Increase the box size or
>   decrease rlist."
> I've increased my box vectors to 100 nm, 100 nm, 100 nm (as I see confirmed
> at the bottom of my .gro file). I am using the Verlet cut-off scheme, which
> as I understand it makes rlist irrelevant and uses its own default cut-off
> length (perhaps of 0.005?), unless I specify verlet-buffer-tolerance = -1.
> I have tried using no verlet-buffer-tolerance line, as well as using
> verlet-buffer-tolerance = -1 and setting rlist = 2. Both of these options
> continue to give the error above.
> How do I check the cut-off length for Verlet scheme? Without being able to
> do that, I cannot confirm that the cut-off length is indeed longer than
> half the shortest box vector. That said, I would be surprised if the
> cut-off length was longer than 50 nm.
> I'm happy to include copies of any files that you feel are necessary to
> understanding this problem. At this point it seems the only information
> necessary are the box vectors and cut-off length (and in this case the fact
> that I'm using Verlet), but I may be wrong.
> Any insight is much appreciated.

Post the full text of your .mdp file.  rlist isn't the only cutoff that matters. 
rcoulomb and rvdw can trigger the problem, too.  There's clearly something weird 
going on.



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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