[gmx-users] Analysis programs and PBC.
tsjerkw at gmail.com
Tue Feb 28 09:25:24 CET 2006
Are you absolutely sure that in your case the -pbc nojump option CAUSES the
rotation? Or could it be that your molecule is rotated a bit, and due to a
too large difference between the reference and the starting frame, this
causes weird results (I've had that, but that was definitely my mistake)?
The snippet of code responsible for removing the jumps I know quite well,
and as far as I can see, there is no way that the routine can cause
rotations. It only shifts over the lattice vectors... (but can really screw
things up if treated the wrong way) If you could send David :p (or me) the
reference structure you use (converted to .gro|.pdb for size and clarity)
and the first frame of the trajectory as you try to process it, dumped as a
.gro|.pdb|.xtc that would allow us to see what is happening.
On 2/28/06, Daniela S. Mueller <D.S.Mueller at rug.nl> wrote:
> Hi Maxim,
> On Mon, 2006-02-27 at 16:56 +0000, Maxim Fedorov wrote:
> > Dear Daniela,
> > > If the molecule you want to analyse is a single molecule, the
> > > jumping of
> > > box boundaries does not matter and the analysis tools take that into
> > > account. But if your molecule is a complex of two or more separate
> > > subunits, you might want to remove jumps over the boundaries to
> > > reassemble the complex again, e.g. to measure the minimum distance to
> > > the periodic images (and not to the subunit, which should be very
> > > nearby).
> > >
> > > What I actually found with trjconv -pbc nojump was, that two
> > > conditionsapply if you want to remove jumps: 1) the trajectory has
> > > to start at the
> > > initial frame and be continuous; 2) the tpr-file should correspond to
> > > the initial conformation. If these conditions weren't fulfilled,
> > > one of
> > > the subunits was rotated and the complex was reassembled
> > > incorrectly -
> > > although the box was rectangular.
> > > This incorrect rotation seems to be a weird bug, probably the
> > > referencing to the tpr-structure is a special case-treatment and not
> > > robust to various setups...?
> > Thank you very much for this information.
> > Could you specify in more details what do you mean when you
> > Could it be residials of a polypeptide/protein chain or
> > you mean something else?
> The protein consists of two chains. During the simulation, one of the
> chains jumped across the box boundary while the other one stayed on the
> original side of the box. After using trjconv -pbc nojump on a
> trajectory fragment starting at a time after the jump, the chain is
> transformed into the box but with a rotation.
> It's pretty tricky because you have to be able to recognise this as the
> wrong assembly, otherwise you would just continue working with a wrong
> I will see if I can submit a bugzilla.
> > All the best,
> > Maxim.
> > >
> > > Success and best regards,
> > > Daniela
> > >
> Daniela S. Mueller
> biologist (Diplom, German degree)
> - Molecular Dynamics Group, UQ -
> School of Molecular and Microbial Sciences (SMMS)
> Chemistry Building (#68)
> University of Queensland
> Qld 4072, Brisbane
> Phone: +61-7-33653732
> Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm
> - MD group, RuG -
> Molecular Dynamics
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Website: http://www.rug.nl/gbb/md
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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