Thanks Tsjerk for the information. It would be very nice if you can elaborate it. I am unable to understand.
-- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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 >
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