[gmx-users] Error in MD

[Tsjerk Wassenaar]

Hi,

> 2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8
> >
> > WARNING: No boxtype specified - distance condition applied in each
> dimension.
> > If the molecule rotates the actual distance will be smaller. You might
> want
> > to use a cubic box instead, or why not try a dodecahedron today?
>
> Unless you can say why you want a triclinic box (the default), while
> you're learning I strongly recommend a cubic box... use the -b option
> appropriately.
>
>
Actually, it would be good to get yourself used to the rhombic dodecahedron
as a default (-bt dodecahedron). It's relatively small and you'll avoid 'box
corner effects'. So, especially for beginners, there's no box like a rhombic
dodecahedron box.

Cheers,

Tsjerk

--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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