[gmx-users] g_msd and diffusion coefficent
mark.abraham at anu.edu.au
Tue Jun 29 10:36:29 CEST 2010
----- 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.
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