[gmx-users] gmx trjconv -center not working?
jalemkul at vt.edu
Thu Feb 7 19:53:48 CET 2019
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
> 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
>>> -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
>> Lab: 303 Engel Hall
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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