On Wed, May 22, 2013 at 4:49 PM, Yutian Yang <yyan...@syr.edu> wrote:
> Erik, > > Do you mean that if the particle diffuses too fast, it will appear like it > doesn't move because of the PBC? > Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the > same as the box length. It is possible that the COM diffusion of the chain > may appear it does not move or move backward due to PBC, right? > Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
