Hi, There is something interesting concerning these MSD calculations. If I treat Centre of Mass MSD if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. And it's true for all my three cases, in which I performed simulation of different times. Is that possible there is some bug in MSD? Because as for me it looks so.... Hope to have someone join the discussion, Slawomir
Wiadomość napisana przez Sławomir Stachura w dniu 2011-12-04, o godz. 22:38: > > Hi, > > I was just wondering how MSDs in Gromacs are normalized. I am calculatiing > MSDs for my lipid system of different timesteps of simulation and I get much > higher results for centre of mass calculations in comparison to mass-weighted > one. And I thought about normalization issue, but I couldn't find any > informations concerning that topic in manual. > I'd be grateful if someone could explain how mean square displacement is > normalized. > > Cheers, > Slawomir -- 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
