[gmx-users] g_msd and diffusion coefficent

leila karami karami.leila1 at gmail.com
Mon Jun 28 12:00:48 CEST 2010

Hi gromacs users

I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent
of pr to dna. I raed manual (g_msd) in which there are  diffusion
coefficent only for 1 and 2 dimension as follows respectively :

-type : Compute diffusion coefficient in one direction: no, x, y or z

-lateral : Calculate the lateral diffusion in a plane perpendicular to: no,
x, y or z
how to use g_msd for calculation of diffusion coeffcient in 3D.

Thanks a lot in advance.
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