[gmx-users] gmx trjconv -center not working?
Mala L Radhakrishnan
mradhakr at wellesley.edu
Fri Feb 8 14:03:49 CET 2019
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.
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
> >>>>>>
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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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> >> --
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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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