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

[Mala L Radhakrishnan]

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.

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981