[gmx-users] g_cluster, RMSD distribution

[Michał Koliński]

Dear All

I’m trying to obtain RMSD distribution of  a ligand in the binding site of the receptor protein during 40 ns MD simulation.
Could you please explain:

- what is exactly the yaxis unit  of the plot obtained using g_cluster with –dist option
-  how is this distribution calculated?

Thank you in advance,

All best,
Michal