[gmx-users] Error in MD
Mark.Abraham at anu.edu.au
Thu Dec 15 12:19:43 CET 2005
Tsjerk Wassenaar wrote:
>>2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8
>>>WARNING: No boxtype specified - distance condition applied in each
>>>If the molecule rotates the actual distance will be smaller. You might
>>>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
> 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.
Tsjerk's point is fair, however you need to make the decision to use a
non-cubic fully aware that (unfortunately) there exist non-gromacs
analysis & visualization tools that won't cope with non-cubic periodicity.
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