Re: Simulation with non-periodic boundary condition

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Thu Jun 19 2008 - 15:15:47 CDT

You can use PBC only with unit cells that tessellate R^3; a truncated
octahedron is one such shape that is also fairly close to a sphere.
There are directions on how to use PBC with a truncated octahedron cell
elsewhere on this list.

Regards,
Victor

On Thu, 2008-06-19 at 19:36 +0100, S.K. Ghosh wrote:
> Dear users,
>
> I am stuck over a basic consideration. I am doing a simulation of
> streptavidin-biotin complex in an ionized water sphere covering the complex
> and also padding it on all sides. But I am using non-periodic boundary
> conditons, since I could not figure out how to use periodic boundary
> conditions with water sphere. Is non-periodic boundary condition a
> reasonable approach for a realistic simulation of biological systems?
>
> Your inputs will be very helpful and appreciated.
>
> Sourav
>

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