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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