[gmx-users] Simulations box type
jalemkul at vt.edu
Wed Apr 17 15:45:42 CEST 2013
On 4/17/13 7:57 AM, raghav singh wrote:
> Hello All,
> I am here not with a problem but still i need your suggestions.
> I have a linear DNA molecule of 200nm in length and want to rum MD to
> calculate some bending properties.
> I want to know ...what kind of solvation box type will be good for such
Consider the DNA molecule to be a rigid rod in its fully extended configuration.
How might such an object rotate? If you envision it rotating with spherical
symmetry, then you have your answer. A cubic box would be a waste, but a
dodecahedron or octahedron would fit quite nicely.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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