[gmx-users] RMSD of Different Simulations

[Mark Abraham]

On 09/02/10 10:20, V Hariharan wrote:
> Hello All,
>
> I've taken the average peptide structure from two different MD
> simulations using g_rmsf.  Is there a method for calculating the RMSD
> between those two structures? The only difference between the two
> peptides is a single residue mutation.  Thanks.

You may need to use trjconv to strip both down to a common matching set 
of (say) CA atoms. Then g_rms -s A.gro -f B.gro.

Mark