Hi Chandan, Pretty simple; you just take the smallest distance between the time points in the periodic system.
Cheers, Tsjerk On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury <iitd...@gmail.com> wrote: > > Dear gmx_users, > > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the > PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer > and at some point of the trajectory, some lipid molecules, due to PBC in the > lateral direction, might pop out from one side of the box and re-ener from > the other side. I such a situation it should show a very lage msd, but > actually in the g_msd code, this fact is taken care of. Can some one > explain, how is this effect taken care of. > > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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