NMSIM finished. Results can be downloaded below.

Prepared PDB-File: 4AKE
Parameters for: Radius of gyration-guided motions

       FIRST:
E-cutoff for H-bonds (kcal/mol): -1
Hydrophobic cutoff (Å): 0.35
Hydrophobic method: 3
RCNMA:
NM-Method: rcnma
Cutoff for C-alpha atoms (Å): 10
NMSIM:
No. of trajectories: 1
No. of NMSIM cycles: 1
Side-chain distortions: 0.3
No. of sim. cycles: 500
Output frequency: 1
NM modes range: 1-50
ROG mode: 1
ROG-guided sim. type: LC
Step size: 0.5
      Trajectory File


      Rigid Cluster Decomposition


Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org

Color-coded representation of the Rigid Cluster Decomposition. The largest rigid cluster is shown in blue.

      
Ensemble showing motions over the trajectory


Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org

Conformations extracted at equally spaced intervalls from the NMSim trajectory. The starting structure is depicted in blue, the ending structure in green, all other conformations corresponding to the secondary structure elements. Simulated movements of the protein can be animated within the JMol Plugin using Mouse -> Right click -> Animation -> Play.

      

RMSD Data File

      
RMSF Data File