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

[Mala L Radhakrishnan]

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...

Mala

On Wed, Feb 6, 2019 at 12:59 PM Benson Muite <benson.muite at ut.ee> wrote:

> Hi,
>
> There are a few issues related to gmx trjconv -center:
>
> a)
>
> http://redmine.gromacs.org/projects/redmine-platform/search?all_words=1&attachments=0&commit=Submit&issues=1&options=0&page=1&q=-center&scope=all&titles_only=&utf8=%E2%9C%93
>
> b) http://redmine.gromacs.org/issues/2579
>
> but not sure if the exactly match what you have.
>
> Benson
>
> On 2/6/19 7:39 PM, Mala L Radhakrishnan wrote:
> > ...and as a follow up, it doesn't seem to be centering at either the
> > geometric center OR the center of mass.  Any insight would be
> appreciated.
> >
> > Mala
> >
> > On Wed, Feb 6, 2019 at 10:15 AM Mala L Radhakrishnan <
> mradhakr at wellesley.edu>
> > wrote:
> >
> >> 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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> >>>> posting!
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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
> >>> --
> >>> 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
> >>
> >
> --
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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