[gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Justin Lemkul jalemkul at vt.edu
Thu Apr 20 20:07:44 CEST 2017

On 4/20/17 9:12 AM, Priyesh Mohanty wrote:
> Dear Justin and Chris,There appears to be no difference between the old and
> the newly created .tpr files. I determined this using gmxcheck. As an
> additional confirmation I reperformed a production simulation of Ubiquitin
> using the old .tpr which originally gave the proper occupancies for a given
> salt bridge. The reperformed run also shows the increase in occupancy
> compared to the original run. I think this suggests a problem with mdrun.

That's a rather serious allegation.  mdrun undergoes correctness testing so that 
the physics is faithfully performed.  Does your GROMACS installation pass all 
the tests after you have installed?

> This problem appeared simultaneously across across multiple machines. The
> stability is more than three times higher in the newer run with the same
> corrections (53% vs 16% occupancy using a 5 angstrom cutoff).

How long are your simulations?  Can you reproduce the findings across multiple 
trajectories starting from different initial coordinates or velocities?  You may 
just have a sampling problem.  Have you tested the correctness of the force 
field modifications by e.g. comparing a single point energy in GROMACS with one 
done in AMBER?



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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