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

[Gyorgy Hantal]

Hi,

I also had that experience with trjconv with various versions. I ended up
doing the centering by a script.
I know on the other hand that centering works well in the case of for
example gmx density. Yet I've had no luck with trjconv...
Maybe this is known issue..?

Regards,
Gyorgy

On Tue, 5 Feb 2019 at 20:27, Mala L Radhakrishnan <mradhakr at wellesley.edu>
wrote:

> Hi again,
>
> As a follow up to my earlier email -- I added -pbc atom to the flags, for a
> total command line of:
>
> gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
> INDEX.ndx -pbc atom -center
>
> This brought it "closer" to the group I chose being centered, but it is
> still not centered at the geometric center of the group I chose.   I'm not
> sure why including -pbc atom would make things different from not including
> it in this case, either.  Any help would be appreciated.
>
> Mala
>
> On Tue, Feb 5, 2019 at 11:37 AM Mala L Radhakrishnan <
> mradhakr at wellesley.edu>
> wrote:
>
> > Hi,
> >
> > I am trying to extract snapshots and center on a particular group, but
> the
> > center of the box does not correspond to the geometric center of the
> group
> > as expected.  It is centered on the outer edge of the group.  Here is the
> > command I am using:
> >
> > gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
> > INDEX.ndx -center
> >
> > ...and I then choose the group in the index file that corresponds to what
> > I want right in the center; I have verified the correctness of the index
> > file.  I ran my simulation with pbc but in this case I specifically want
> to
> > maintain the same cubic box used in the simulations, so I don't want to
> > keep molecules whole.  So all I want to do is extract the cubic box that
> is
> > centered on the group I want.   But the resulting snapshot has the
> molecule
> > slightly (about 10%) off center, mainly in the y direction in this
> case.  I
> > presume that center will place the geometric center of the group you
> choose
> > at the geometric center of the box.  Am I incorrect?  Is there another
> way
> > to accomplish what I want?
> >
> > Thank you so much,
> >
> > Mala
> >
> >
> > --
> > Mala L. Radhakrishnan
> > Whitehead Associate Professor of Critical Thought
> > Associate Professor of Chemistry
> > Wellesley College
> > 106 Central Street
> > Wellesley, MA 02481
> > (781)283-2981
> >
>
>
> --
> Mala L. Radhakrishnan
> Whitehead Associate Professor of Critical Thought
> Associate Professor of Chemistry
> Wellesley College
> 106 Central Street
> Wellesley, MA 02481
> (781)283-2981
> --
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-- 
---------------------------
Gyorgy Hantal, PhD
Postdoctoral Fellow
Dept. of Computational Physics, University of Vienna
Sensengasse 8/9, 1090 Wien, Austria
gyorgy.hantal at univie.ac.at <gyorgy.hantal at gmail.com>
Tel. +43-(0)1-4277-73292