[gmx-users] RMSD of MD run

[Nguyen Hoang Phuong]

> Hi,
>
> 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
> simulation?
> 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.
>
I would suggest to do the principal component analysis and look at the
free energy surface built by first few principal components.

Phuong



> --
> ------------------------------------------------------
> Ran Friedman
> Laser laboratory for fast reactions in biology
> Department of biochemistry
> Faculty of life sciences
> Tel-Aviv university
> 972-3-6409824
> ------------------------------------------------------
>
>
>