[gmx-users] gmx trjconv -center not working?

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 19:45:47 CET 2019

On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote:
> Thanks...but these don't really address the issue I have.  I've written my
> own script now to do re-centering and looping of atoms across the box walls
> myself, but I am still really unclear why -center does not in fact center
> the molecule in the box either at its geometric center OR its center of
> mass (I have written scripts to test both out and neither match, and
> visually the molecule is clearly not centered in the box)
> To me it definitely seems like something is not right with this utility or
> something about the options I've used are conflicting in ways I don't
> understand:
>   -pbc atom -center (a group from index file)
> Thanks again for any other ideas...

I've only been loosely following this thread, but I've never had a 
problem where trjconv didn't center as I wanted. Have you verified that 
the index group is correct, and you're making the proper selection? What 
does gmx traj report as the center-of-mass coordinates for those groups 
before and after trjconv tries to center them?



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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