[gmx-users] gmx trjconv -center not working?
Justin Lemkul
jalemkul at vt.edu
Fri Feb 8 14:18:19 CET 2019
On 2/8/19 8:15 AM, Mala L Radhakrishnan wrote:
> Hi Justin,
>
> Also -- this is important, I need to maintain the shape of the cubic box,
> so I do *not* want to keep molecules at the box edges whole (I know this
> sounds weird, but I need it for my applications) -- so should I use -pbc
> atom instead of -pbc mol for the first step?
The shape of the box will not change with any of the -pbc options, you
may just have a few atoms sticking "out" of the actual dimensions
depending on PBC treatment. But the *box* never changes unless you
re-wrap or manipulate it with -ur (though, as I've said for a cube, you
can't really actually change).
-Justin
> Thanks again so much -- just want to make sure before I start making these
> huge files :)
>
> Mala
>
> On Fri, Feb 8, 2019 at 8:07 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
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>> before
>>>>>>>>>> posting!
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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
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>>>>>>>> posting!
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>>>>>> --
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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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>>>> Gromacs Users mailing list
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>>>> * Please search the archive at
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>>>> posting!
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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
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>> posting!
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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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