[gmx-users] Instantaneous Square Displacement

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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