[gmx-users] View Trajectory - Water Expansion

Justin Lemkul jalemkul at vt.edu
Thu Feb 11 13:41:27 CET 2016

On 2/11/16 7:13 AM, Natalie Stephenson wrote:
> Hi all,
> I'm experiencing a problem with my trajectory waters. Really early on in the simulation the waters begin expanding out of the box. There are no system errors that I am aware of and the simulation runs fine.
> Is this something that can be fixed with trjconv? Or is it something more worrying with regards to the simulation run? I'm currently using trjconv with -pbc nojump, resulting in the protein looking fine, but the waters are another matter.

Waters are diffusing "out" of the box (which can't actually happen) as a result 
of using -pbc nojump; that's it's function.



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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