[gmx-users] RMSD value

[Mark Abraham]

On 9/01/2012 8:26 PM, madhumita das wrote:
> Hi GROMACS Users,
>
>                                   I have simulated a protein(pdb id 
> 3D9S) for 5 nanoseconds. This protein contains 978 residues and after 
> 5 nanoseconds I got 2.35 by comparing pdb structure with simulated 
> one. I want to know is this value is ok or protein is disrupted?

Visualize your trajectory to get a handle on what this number means.

Mark