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