[gmx-users] how to calculate redisue wise RMSD in gromacs?

[Mark Abraham]

yren at home.ipe.ac.cn wrote:
> Dear friends,
>  I have carried out a simulation of a protein in solution and want to
> analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As
> far as I know,   RMSD can be calculated by g_rms, which gives RMSD as a
> function of time, but what I expect is RMSD as a function of residue
> number. It's said that AMBER has this function. I wonder whether gromacs
> can do this also.

Check out "g_rms -h", in particular the -ng option. I expect you can use
this in concert with an index file that has a group for each residue.

Mark