[gmx-developers] trjconv -fit rot+trans -pbc broken, was: trjconv defaults

[Roland Schulz]

Hi,

I'm replaying here to a year old thread because I found Tsjerk desribing a
problem I'm currently having and I think no fix is so far planned.

As he describes below if you do a fit then a later pbc correction is wrong
because the box vectors don't get rotated together with the system.

But this problem is not only introduced by changed defaults (as -ur compact)
but is a problem with any -ur.

Whenever one does a trjconv -fit rot+trans -pbc [any pbc] the pbc correction
is wrong because the box vectors are wrong.

Doing the pbc before is not a work-around because the rotation might move
molecules out of the box again. Also first doing the fit and the calling
trjconv again for -pbc does not work because the saved box vectors are the
wrong (unrotated) ones and thus the pbc still are wrong.

The only fix I see is Tsjerk's solution to also rotate the box vectors. Or
is there any other solution?

Roland


On Fri, Oct 17, 2008 at 4:02 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi,
>
> No!
>
> I was already typing that I was in favour of setting -pbc to whole by
> default, but not -ur compact, when the following struck me: Setting
> these to defaults will screw up any trajectory/pdb which has before
> been processed with options causing discrepancy between configuration
> and pbc. In normal words, whenever you've performed a fit, you'll only
> end up with garbled output running trjconv again.
>
> The solution to that, and I mentioned that to Erik at the workshop,
> would be to have all fitting and other reorienting procedures also
> perform on the box. That's a minor change, but then again, we have to
> get rid of the 'box too skewed' error in analysis tools and be
> prepared to use all nine numbers in the box matrix for the definition
> of the PBC. Note that this doesn't work for PDB files, and there is no
> work-around.
>
> In the margin of that, I also disfavour having the default for -ur set
> to compact, because it will give unnecessary computational overhead
> when processing trajectory files for whatever. Resetting to a
> rectangular brick (or triclinic cell) on the other hand, is trivial.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Oct 17, 2008 at 10:19 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
> > Hi,
> >
> > shall we set the trjconv defaults to -pbc mol -ur compact ?
> > Even I get fooled when dumping a pdb file and suddenly noticing that it
> is
> > broken.
> >
> > Cheers,
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Professor of Biology
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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