[gmx-users] Instantaneous Square Displacement

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 8 07:25:46 CET 2011

On 8/03/2011 3:01 AM, Jennifer Williams wrote:
> Hi,
> I am writing a paper where I describe that gas molecules move inside a 
> pore and then stick for long periods of time in occlusions in the pore 
> wall.
> A reviewer has mentioned that I could illustrate this effect by using 
> "instantaneous square-displacement".
> I have already produced MSD vs time plots and used them to obtain the 
> self diffusion coefficient. Can someone shed some light on how I can 
> obtain the instantaneous square displacement in gromacs?

I have no idea what "ISD" means, and Google doesn't know either :) 
Perhaps they want to see the diffusion of a single molecule?


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