[gmx-users] warning in editconf

[Justin A. Lemkul]

leila karami wrote:
> Hi
> 
> for making simulation box for pr-dna interaction I typyed  [editconf -f 
> -o -d 0.5] but this warning appeared:
> 
> 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?
> 

You either need to specify a box type (-bt) or use the -d flag such that it 
satisfies the minimum image convention in the case of your molecule rotating, as 
editconf has clearly warned you.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

> please guide me.
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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