[gmx-users] RE: g_msd and diffusion coefficent

[Vitaly Chaban]

> Dear Vitaly Chaban
>
> yes. my md simulation is equilibrioum.
>
> I did simulation of protein-dna. I want to know how protein and dna close
> together and interact together (approach of protein to major groove of dna).
>
> thanks alot in advance.


Dear leila,

Please look towards g_rmsdist utility of the gromacs package. This
seems to be better for your needs than g_msd.

Good luck.
Vitaly

Dr. Vitaly Chaban