> > 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. >> >
In periodic system, there is infinite number of images of each particle. You should always consider the smallest possible distance [between the image of the two particles]. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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
