[gmx-users] Two-body Bonded Distance

Justin Lemkul jalemkul at vt.edu
Mon Mar 3 18:46:46 CET 2014

On 3/3/14, 9:26 AM, jolayfield wrote:
> Justin,
>     The two-body distance is about 4x the actual distance in the structure
> file.  This spuriously large distance only appears once I add the virtual
> particle.  This appears to not affect the actual MD run based on my tests
> with and without the virtual particle, but it does limit the number of
> processors that I am able to use during the run.  Is there a reason that the
> distance should be different for the two-body bonded and multi-body bonded
> distance when they span the same atoms?

Where are you adding the virtual particle in relation to all of this?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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