[gmx-users] Query of RMSD results

[Sainitin Donakonda]

Hello,

I performed 20ns MD simulation on 2 types systems

1) Protein only
2) Protein-ligand 1 complex

Then did RMSD analysis on both systems i observed that following RMSD mean
as follows

Protein only : 0.45 nm
Protein-ligand 1 complex: 0.40

Now i am confused how to interpret this result as protein-ligand complex
RMSD is lower than apo form of protein.

Can any body please explain how to explain these results

Thanks,
Sainitin