[gmx-users] Significance of box vectors in GRO trajectory file.

[Justin Lemkul]

On 6/5/17 10:07 AM, Dawid das wrote:
> Dear Gromacs Users,
> 
> Suppose I have a trajectory file in gro format. If I change the last line
> for each
> snapshot (i.e. line with box vectors values) into an arbitrary set of three
> numbers,
> will it have impact on further manipulations of this gro trajectory file
> with trjconv?
> 
> In other words, is the line with box vector significant for a following
> command:
> 
> gmx trjconv -f npt-md2-system.gro -o npt-md2-0-0.5ns.gro -s npt-md2.tpr
> -ndec 6 -pbc mol -center
> 
> ?
> I especially worry whether it is going to be fine for -pbc mol and -center
> options.
> Do they read this vector at all?

Yes, the box vectors are used for reimaging and if you change them you will 
change both the centering and re-wrapping of coordinates.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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