Thanks! So, how much do I "pay" for the periodicity? Is the memory times 8? What about restraint evaluation? 

Also, do you know how they do it in popular MD softwares? Do they keep 28 images, or just evaluate the energy function periodically?

On Fri, Nov 15, 2013 at 2:46 PM, Riccardo Pellarin <pellarin.riccardo@gmail.com> wrote:

Yes... And sorry for the typo, you need 26 clones if you want to have a 3D periodic system (8 clones is for 2D).

On Fri, Nov 15, 2013 at 2:20 PM, Ben Webb <ben@salilab.org> wrote:

On 11/15/13 2:16 PM, Riccardo Pellarin wrote:

Actually that is already doable using the
IMP::core::TransformationSymmetry score state (or particle state?).
For your XYZ box, copy your system into 8 clones, and apply a different
TransformationSymmetry to each of them,

Right, but that's not PBC, it's periodic images. It would achieve the same result though...

        Ben
--
ben@salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
        - Sir Arthur Conan Doyle

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