[gmx-users] RMSD of MD run

Ran Friedman ran at hemi.tau.ac.il
Thu Nov 6 10:56:01 CET 2003


I've made a 3ns  md run of a system consisting a protein, a small
ligand, water and some salt molecules.
The backbone RMSD of the protein was stable during the first 2ns, with a
maximum value of 1.8nm. Most of the time the RMSD was ~1.5nm.
After ~2ns, the RMSD started rising. It reached ~1.95ns at 3ns.

My question is:
1. Does this necessarily means that there's something wrong with my
2. If it doesn't, how can I verify it (i.e. how can I make sure that the
protein undergoes a some kind of a conformational change)?

I'd appreciate any help,

Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university

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