[gmx-users] editconf and g_rmsdist

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Sep 18 13:20:51 CEST 2009

Hi Soren,

>  Why I am seeing this difference? Is it due to round-off’s after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
> wrongly?

It's a bit weird indeed. You might be right that it's due to round-off
errors. You can try to copy the original gro file and replace the last
line with "   4.00000   4.00000   4.00000" to set the box manually.
That should rule out whether it's the box, which I can hardly imagine.
The other test is to add a shift, but you'd want to make sure that
rounding could get an issue then...

Hope it helps,


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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