[gmx-users] gmx trjconv -center not working?
Mala L Radhakrishnan
mradhakr at wellesley.edu
Fri Feb 8 14:32:11 CET 2019
...and molecules at the edges can totally be broken. So really just a
translation of the box coordinates to be centered on the desired group. It
should really be very straighforward.
If it's easier to take offline, I'm happy to.
M
On Fri, Feb 8, 2019 at 8:29 AM Mala L Radhakrishnan <mradhakr at wellesley.edu>
wrote:
> Hi Justin,
>
> Yes, but I don't want anything sticking out of the box. I need the shape
> of my entire system, when visualized, to be wholly contained within the
> cubic shape -- and centered on the desired group. That's pretty much all.
> Does this clarify? Does this change what you recommend?
>
> Mala
>
> On Fri, Feb 8, 2019 at 8:18 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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!
>> >>>>>>>>>>
>> >>>>>>>>>> * Can't post? Read
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>> >>>>>>>>>>
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>> >>>> 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
>> >>>>>>>>
>> >>>>>>>> ==================================================
>> >>>>>>>>
>> >>>>>>>> --
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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
>> >>>>
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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
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
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>> >> 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
>>
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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
>
--
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981
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