[gmx-users] Error in MD

[Mark Abraham]

Tsjerk Wassenaar wrote:
> 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.

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.

Mark