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