[gmx-users] Instantaneous Square Displacement

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 8 12:27:00 CET 2011

Mark Abraham wrote:
> 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?

Searching for "instantaneous square displacement" turns up very little (3 
results), but the last seems to be what you need, as long as this person is correct:


Section 2.3.3.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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