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

[Benson Muite]

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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>>>>
>>>
>>> --
>>> ---------------------------
>>> 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
>>
>