Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions.
Erik On 22 May 2013, at 11:41, 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
