> Also, do you know how they do it in popular MD softwares? Do they keep 28 images, or just evaluate the energy function periodically?
charmm can do both. However periodic images is very general and can be used for any weird symmetry, and PBC only for boxes.
On Fri, Nov 15, 2013 at 4:27 PM, Riccardo Pellarin < pellarin.riccardo@gmail.com> wrote:
> 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.comwrote: > >> 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 >> > >