Thanks for this Vitaly and Justin. George > The resulting MSD will correspond to the average from individual atoms. > > Calculating MSD of an individual atom and ascribing it to a [small] > molecule, which this atom belongs to, is reasonable. Assuming that > averaged > MSD from atoms correspond to the cluster they form is not. > > > Dr. Vitaly Chaban > > > > > On Wed, May 1, 2013 at 2:40 PM, George Patargias <g...@bioacademy.gr> > wrote: > >> Hello >> >> I am trying to calculate the MSD of 8 molecules in a lipid bilayer with >> g_msd. If I include the atoms of all these 8 molecules as a single group >> in the index file, will g_msd calculate the MSD of the center of mass of >> them or it will average over all atoms? >> >> >> Thanks >> George >> >> >> Dr. George Patargias >> Postdoctoral Researcher >> Biomedical Research Foundation >> Academy of Athens >> 4, Soranou Ephessiou >> 115 27 >> Athens >> Greece >> >> Office: +302106597568 >> >> >> >> >> >> >> -- >> 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 >> > -- > 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 >
Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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
