[gmx-users] gmx trjconv -center not working?
Mala L Radhakrishnan
mradhakr at wellesley.edu
Fri Feb 8 14:29:19 CET 2019
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
> >>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> >> before
> >>>>>>>>>> posting!
> >>>>>>>>>>
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> >>>>>>>>>>
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> >>>>>>>>>>
> >> 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
> >>>>>>>>
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> before
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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
> >> 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
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> 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
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