----- Original Message ----- From: leila karami <[email protected]> Date: Tuesday, June 29, 2010 17:32 Subject: [gmx-users] g_msd and diffusion coefficent To: [email protected]
> 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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