[gmx-users] gmx trjconv -center not working?
Justin Lemkul
jalemkul at vt.edu
Fri Feb 8 12:55:59 CET 2019
On 2/8/19 6:52 AM, Mala L Radhakrishnan wrote:
> Hi Paul,
>
> Thanks for this idea --
>
> ...But it returns what I would expect:
>
> Statistics over 1 steps [ 200000.0000 through 200000.0000 ps ], 3 data sets
> All statistics are over 1 points
>
> Energy Average Err.Est. RMSD Tot-Drift
> -------------------------------------------------------------------------------
> Box-X 12.2482 -- 0 0 (nm)
> Box-Y 12.2482 -- 0 0 (nm)
> Box-Z 12.2482 -- 0 0 (nm)
>
> This matches what the pdb extracted file says (i.e. the file which does not
> have the complex centered at the Box-X/2, Box-Y/x, Box-Z/2)
> So I'm still not sure what's going on -- any other thoughts?
From your trjconv command, it looks like you are somewhat inefficiently
trying to simply output the final frame, is that correct?
I have found quirky behavior in trjconv when trying to do multiple
actions (you're centering and manipulating PBC at the same time) while
also skipping many frames. Here's what I would suggest:
gmx trjconv -s md.tpr -f md.xtc -pbc mol -o md_mol.xtc
gmx trjconv -s md.tpr -f md_mol.xtc -center -o md_center.xtc -n index.ndx
gmx trjconv -s md.tpr -f md_center.xtc -dump 200000
Does that improve the situation? If not, please send a minimal test case
to me off-list and I will take a look.
-Justin
> Mala
>
>
>
> On Fri, Feb 8, 2019 at 5:39 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
>
>> 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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
--
==================================================
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
==================================================
More information about the gromacs.org_gmx-users
mailing list