[gmx-users] Simulations box type

[Justin Lemkul]

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
> molecule??
>

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

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Justin A. Lemkul, Ph.D.
Research Scientist
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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