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?
Thanks
Jenny
Quoting "Justin A. Lemkul" <[email protected]>:
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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