On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
>
> ...one molecule sitting on the box edge or corner happens to cross the
> boundary in two different dimensions during the same frame change. In
> this scenario the wrapping of the second periodic boundary is not
> accounted for and the MSD jumps up by n * L^2/N (L= simulation box
> length. n= number of molecules in the mask double wrapping that frame,
> and N = the number of molecules in the mask).
Are you trying to compute diffusion behavior from a trajectory that was
originally created with iwrap=1? Or that has been subject to the "image" or
"autoimage" command in cpptraj? Just trying to pin down possible sources of
problems.
....dac
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Received on Tue Mar 08 2016 - 17:00:04 PST
