[gmx-users] Steepest Descents converged to machine precision in XX steps

Justin Lemkul jalemkul at vt.edu
Tue Mar 7 15:11:53 CET 2017

On 3/7/17 9:00 AM, Nikhil Maroli wrote:
> Dear Justine,
> My simulation system is a protein on the surface of the lipid layers, which
> is created using charmm-gui. There are no overlapping between atoms or
> whatsoever. How can i overcome this issue?

Start by visualizing the system right where mdrun is telling you there is an 
issue.  It prints out which atom has the infinite force.  That's usually a clue.


> I have remodelled the system by keeping more distance between protein and
> lipids and that time maximum force on atoms came to be 4E18.
> Thanks


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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