[gmx-users] gmx trjconv -center not working?

Mala L Radhakrishnan mradhakr at wellesley.edu
Fri Feb 8 14:15:37 CET 2019


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?

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!
> >>>>>>>>
> >>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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
> >>>>>>
> >>>>>> ==================================================
> >>>>>>
> >>>>>> --
> >>>>>> 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!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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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