Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks
On Wed, May 22, 2013 at 10:56 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
