[gmx-developers] trjconv defaults

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 17 11:02:12 CEST 2008



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

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.



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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