[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

Justin Lemkul jalemkul at vt.edu
Tue Oct 27 13:01:19 CET 2015

On 10/27/15 7:51 AM, Alan wrote:
> Hi there,
> I used to have this, just for simple quick test:
> cat em.mdp
> integrator               = steep
> nsteps                   = 500
> Alas, it does not work anymore with GMX 5.
>    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.
> And my md.mdp (which I didn’t test yet, and I fear it will likely fail too)
> is:
> integrator               = md
> nsteps                   = 1000
> If I could keep them working for both GMX 5 and 4.5 that would be great.

The error is related to the size of the system; the default value of rlist 
hasn't changed recently (or ever?) from 1.0 nm, so it seems that your bare-bones 
.mdp file could selectively fail if the system is small or the box is 
incorrectly assigned.  Perhaps it's something related to the Verlet scheme 
becoming the default since 4.5?  The only thing that should affect rlist would 
be verlet-buffer-tolerance.



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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