[gmx-users] gmx trjconv -center not working?
Mala L Radhakrishnan
mradhakr at wellesley.edu
Thu Feb 7 19:52:40 CET 2019
I've verified the I'm entering in the right group and that it's correct in
the index file. Where do I find the output for what it thinks is the
center of mass before and after? That would be helpful output, but I
haven't found such output in standard output or error.
thanks again for instructions on how to get this info..
On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > own script now to do re-centering and looping of atoms across the box
> > 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
> > 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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Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
106 Central Street
Wellesley, MA 02481
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