[gmx-users] Two-body Bonded Distance

Justin Lemkul jalemkul at vt.edu
Mon Mar 3 21:28:04 CET 2014

On 3/3/14, 1:52 PM, jolayfield wrote:
>>> Where are you adding the virtual particle in relation to all of this?
> The virtual particle is included in the ligand residue (#160) but this error
> occurs in whichever methionine residue has the longest CB-CE distance.  They
> are not spatially near one another and the offending residue is different
> from trajectory to trajectory given the fluctuations of the MET side chains.

There's no reason that I can think of that adjustments to one molecule should 
affect two-body interactions in a different molecule.  Sounds buggy.  Please 
file an bug report on redmine.gromacs.org with all the files necessary to 
reproduce it so it can be examined.



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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