[gmx-users] Diffusion coefficient
jalemkul at vt.edu
Mon Sep 18 00:15:39 CEST 2017
On 9/17/17 6:05 PM, Dallas Warren wrote:
> Don't know exactly how to do it myself, but there will be an option
> there where you can specify the z coordinate as a way to break it up
> into groups.
And herein lies the challenge. The selections themselves will give index groups
per frame, may vary in size, and the individual molecules themselves will likely
occupy each slice discontinuously with respect to time. So a lot of effort
would have to be made to make per-molecule sub-trajectories to compute a
diffusion coefficient for a given time frame in which the molecule continuously
satisfies the criterion, then calculated again over another period of time if
the molecule moves out and comes back (otherwise one would get a spurious
contribution to the MSD if a molecule seems to jump around). I suppose it can
be done, but only very tediously in reassembling frames to make
sub-trajectories, then looping over every molecule individually in doing so.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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