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

[Justin Lemkul]

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 <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
>> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================