[gmx-users] gmx trjconv -center not working?
Mala L Radhakrishnan
mradhakr at wellesley.edu
Fri Feb 8 15:13:12 CET 2019
ok -- thanks -- am to trying this out now. btw, I am also running 2016.3
to analyze a trajectory made with 2016.4. I tried a couple of versions
and still got the same weird behavior, but I thought I'd let you know in
case you know that using a slightly older version to analyze a newer one is
problematic.
M
On Fri, Feb 8, 2019 at 8:32 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/8/19 8:29 AM, Mala L Radhakrishnan 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?
>
> Use -pbc atom instead of -pbc mol in my first suggested command.
>
> -Justin
>
> > 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!
> >>>>>>>>>>>>
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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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> >>>>>> --
> >>>>>> ==================================================
> >>>>>>
> >>>>>> 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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> >>>>
> >> --
> >> ==================================================
> >>
> >> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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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
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