[gmx-users] gmx trjconv -center not working?
Justin Lemkul
jalemkul at vt.edu
Fri Feb 8 14:06:08 CET 2019
On 2/8/19 8:03 AM, Mala L Radhakrishnan wrote:
> Hi Justin,
>
> Thank you SO much -- I will try this out, but I have a silly question
> before I do -- is there a way to dump just the desired frame in the first
> step itself -- or would that screw up the ordering -- since my xtc files
> are just so huge and I'd rather not create more huge files than necessary?
> If there is no other way, then I will do it, but these are massive files
> and I'd need to create them for many simulations.
You can try, but my suggestion is that you have to be careful in making
leaps from one reference state to a final state. In principle, it should
work no matter what, but I've noticed that trjconv does sometimes
require processing of a full trajectory for PBC and fitting purposes. I
have no explanation as to why, but if you carefully and methodically
invoke trjconv, there should never be a problem getting it to behave as
you need it to.
-Justin
> Thanks,
>
> M
>
> On Fri, Feb 8, 2019 at 6:56 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>>>>>
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>> or
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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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
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>>>>>>
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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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>>
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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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