We run a a 62ns simulation on the 2v0w light state using 32 processors. Here is a video.

Validation of the simulation

Here are the values of pressure, temperature and volume for this run.

The rmsd along the run gives:

And the rmsf is:

Analysis of the simulation

As for the dark state, we tried to find a change in the j-alpha helix then looked at the comportment of the residues.

We ploted the angle between the helix and and a strand of the beta sheet. As in the light state we don't see a clear movement.

An interesting residue to study in the light state is the residue n° 450, which is the cystein that reacts with the cofactor. Here we plot the dihedral angle of this residue to see how many time the cystein point toward the FMN: