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

[Peter Kroon]

What does "gmx energy -b 20000 -e 20000" give as box dimensions?


Peter

On 07-02-19 22:20, Mala L Radhakrishnan wrote:
> Hi Justin,
>
> Thank you -- the good news is that the center of mass of this group does in
> fact match what I calculate to be the COM with my script.
>
> BUT, the bad news is that this is not in the center of the box after I have
> asked for it to be centered (which I presume it should be)::
>
> COM:
> 5.95324    6.00572    5.68943
>
> The cubic box is 12.249 long (as noted in the CRYST1 field of the pdb file
> and its left corner is at the origin (I know this because I have atoms that
> go all the way to the edges of the box and my minimum x,y, and x
> coordinates are basically 0 and my maximum are basically 12.24 in all three
> directions, which would make the center of the box:
>
> 6.1245, 6.1245, 6.1245
>
> So it's close but a few angstroms off.  Can you please tell me what might
> be going on here?  I am happy to share files with, as I'd be really
> grateful for your help.  Again, I've written a scrip to translate and
> "wrap" the atoms across the pbc in the worst case scenario, but I have to
> imagine gromacs should be able to do this correctly.
>
> Again - this is the command I used to extract the hopefully centered frame:
> gmx trjconv -f md.xtc -o all.pdb -s md.tpr -b 200000 -e 200000 -n INDEX.ndx
> -pbc atom -center
>
> ...and I chose the correct index (and extracted the same atoms just in case
> to make sure that I knew exactly what atoms it thought it was centering, in
> case something was in fact wrong with the index file)
>
> Thank you so much,
>
> Mala
>
>
> On Thu, Feb 7, 2019 at 1:54 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote:
>>> Hi Justin,
>>>
>>> I've verified the I'm entering in the right group and that it's correct
>> in
>>> the index file.  Where do I find the output for what it thinks is the
>>> center of mass before and after?  That would be helpful output, but I
>>> haven't found such output in standard output or error.
>> gmx traj -ox -com
>>
>> -Justin
>>
>>> thanks again for instructions on how to get this info..
>>> Mala
>>>
>>> On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote:
>>>>> 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...
>>>> I've only been loosely following this thread, but I've never had a
>>>> problem where trjconv didn't center as I wanted. Have you verified that
>>>> the index group is correct, and you're making the proper selection? What
>>>> does gmx traj report as the center-of-mass coordinates for those groups
>>>> before and after trjconv tries to center them?
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>> * Please search the archive at
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>