Sure. What's the MSD of a pendulum if you only sample at a rate equal to the period? How often you want to sample depends on the time scale of what you want to observe. That might be up to you to measure :-)
Mark On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina < anna.akinsh...@manchester.ac.uk> wrote: > Dear Gromacs Users, > > I have a question interpreting obtained msd data. > I need to calculate diffusion coefficient for a single argon atom in a box > of water (500 molecules). > During the calculations (50ns) I write both trr and xtc trajectories, but > to save space I write trr for whole system very seldom (every 50000 steps = > 100 ps) > but in xtc I have argon only (no water) and write more often (every 1000 > steps = 2 ps). > > When I analysed the results using g_msd I was surprised that the msd > curves obtained from trr and xtc trajectories differ a lot, what affect > the resulting diffusion coefficients. > > If I save trr more often, like every 10000 steps (20ps) the results from > both files coincide. > > Does the msd results depend on how often you write trajectories? > If yes, what frequency for writing the trajectories for future calculation > of the diffusion coefficient would be reasonable and how long should be the > calculations? > > Thanks you > Anna > ----------------------- > Dr Anna Akinshina > School of Chemical Engineering & Analytical Science > The University of Manchester, UK > > > -- > 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
