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

[Mala L Radhakrishnan]

Hi Justin,

Thank you -- the good news is that the center of mass of this group does in
fact match what I calculate to be the COM with my script.

BUT, the bad news is that this is not in the center of the box after I have
asked for it to be centered (which I presume it should be)::

COM:
5.95324    6.00572    5.68943

The cubic box is 12.249 long (as noted in the CRYST1 field of the pdb file
and its left corner is at the origin (I know this because I have atoms that
go all the way to the edges of the box and my minimum x,y, and x
coordinates are basically 0 and my maximum are basically 12.24 in all three
directions, which would make the center of the box:

6.1245, 6.1245, 6.1245

So it's close but a few angstroms off.  Can you please tell me what might
be going on here?  I am happy to share files with, as I'd be really
grateful for your help.  Again, I've written a scrip to translate and
"wrap" the atoms across the pbc in the worst case scenario, but I have to
imagine gromacs should be able to do this correctly.

Again - this is the command I used to extract the hopefully centered frame:
gmx trjconv -f md.xtc -o all.pdb -s md.tpr -b 200000 -e 200000 -n INDEX.ndx
-pbc atom -center

...and I chose the correct index (and extracted the same atoms just in case
to make sure that I knew exactly what atoms it thought it was centering, in
case something was in fact wrong with the index file)

Thank you so much,

Mala


On Thu, Feb 7, 2019 at 1:54 PM Justin Lemkul <jalemkul at vt.edu> wrote:

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