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

Mala L Radhakrishnan mradhakr at wellesley.edu
Fri Feb 8 12:52:51 CET 2019


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?

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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> >> posting!
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> >
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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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