On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote:
Hi Justin,
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.
gmx traj -ox -com
-Justin
thanks again for instructions on how to get this info..
Mala
On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalem...@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
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
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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