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

[Mala L Radhakrishnan]

...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
>> >
>> > * Please search the archive at
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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
>


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