[gmx-users] Diffusion coefficient

Justin Lemkul jalemkul at vt.edu
Mon Sep 18 00:15:39 CEST 2017

On 9/17/17 6:05 PM, Dallas Warren wrote:
> http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
> 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.
Assistant Professor
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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