[gmx-users] g_msd and diffusion coefficent

[Mark Abraham]

----- Original Message -----
From: leila karami <karami.leila1 at gmail.com>
Date: Tuesday, June 29, 2010 17:32
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users at gromacs.org

> Dear Mark Abraham  >   > yes. pr means protein. I want to obtain diffusion of  protein within dna. I  want to know how/how much pr diffuse to dna.

No, you probably don't. "within" and "to" mean different things. You probably want to measure something about the diffusion of your protein in water (the solvent!) in the presence of DNA.

If you're trying to deduce something about the frequency of protein-DNA binding events, then you'll probably need a ridiculously long and large simulation with lots of such events in order to deduce anything comparable with any experimental data.

Mark

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