[gmx-users] Instantaneous Square Displacement

Jennifer Williams Jennifer.Williams at ed.ac.uk
Wed Mar 9 14:04:17 CET 2011

Thanks for the advice. I has also found that last source on google and  
have been thinking how I could apply this.

I assume that if I plotted [rt - r0]^2 against time then (for a single  
molecule) I would get peaks on the graph when the molecules are mobile  
and dips (where [rt-r0]^2 is close to zero) for the periods where  
molecules are stuck.

This would seem to make sense only for a single molecule (as Mark  
suggested) as averaged over all molecules, the peaks and troughs would  
average out and I wouldn't really be illustrating anything.

I have made a rough sketch of what the plot should look like and for a  
few moves of the molecules (using only 15 positions) it seems to make  
sense. However I don't really find it intuitive given that iSD isn't  
widely used and for more than a few moves it gets crowded and  
difficult to interpret.

So as I see it, the graph would sample only one molecule over a short  
time period.

Any more thoughts on this?



Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> 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:
> http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1
> Section 2.3.3.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
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