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

[Mala L Radhakrishnan]

Hi,

It would be helpful to know if this is a known bug/issue.  I'd rather not
have to write code to recenter in this case -- would be easy if I just had
one molecule far from the edges of the box but I am simulating a crowded
system and need to get it centered on one complex within the system while
still maintaining the cubic shape of the box -- I suppose I could write a
script to pass atoms from one side of the box to the other as a result of
the translation, but the box size slightly changes at each step (it's an
NPT simulation) and I fear I'd be messing things up -- so I'd really rather
not have to do that if there is actually a way with -center.  I can't get
anything to work the way the documentation says it's supposed to.

Does anyone out there know if this is a known bug?  Any of the developers,
perhaps?

Thanks,

Mala

On Wed, Feb 6, 2019 at 9:30 AM Gyorgy Hantal <gyorgy.hantal at univie.ac.at>
wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
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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
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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