[gmx-users] Re:g_msd and diffusion coefficent

[Vitaly Chaban]

> Message: 5
> Date: Tue, 29 Jun 2010 11:54:12 +0330
> From: leila karami <karami.leila1 at gmail.com>
> Subject: [gmx-users] g_msd and diffusion coefficent
> To: gmx-users at gromacs.org
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> Dear Vitaly Chaban
>
> I know using index file but gromacs say : select only 1 group. what is this
> group ? protein? or DNA?


It is not clear what exactly you want. To observe as one molecule
moves in relation to another one? If this would have been my task, I
would introduce some specific function of the distance between them vs
time. Is it not easier just to calculate two diffusion constants
corresponding to your particles of interest?

Is it equilibrium MD that you perform?

Vitaly