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
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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