It's a bit pricey memory-wise, if you system is big. Score evaluation is a bit less efficient, but not so much if you are careful in selecting non-redundant score terms.
On Fri, Nov 15, 2013 at 4:24 PM, Barak Raveh barak.raveh@gmail.com wrote:
> 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 >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> > > > -- > Barak >