[gmx-users] MSD and frequency of writing trajectories

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

Re: [gmx-users] MSD and frequency of writing trajectories

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

Re: [gmx-users] MSD and frequency of writing trajectories

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