[gmx-users] g_msd and diffusion coefficent

[Mark Abraham]

----- Original Message -----
From: leila karami <karami.leila1 at gmail.com>
Date: Tuesday, June 29, 2010 18:08
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users at gromacs.org

> Dear Mark Abraham> No, I want to measure something about the diffusion of my protein to DNA (especially  to major groove of DNA) in the presence of water (as solvent).
Well if you have a trajectory that diffuses the protein to your DNA, then measure the diffusion coefficient by choosing the protein group in g_rmsd. The analysis program doesn't need to know why you chose that trajectory.

Finding a meaningful set of such a trajectories can be tough, however.

Mark

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