This extension computes the nonlinear normal modes of a molecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021/acs.jctc.7b00197).

The user indicates the desired number of modes, the interactions cutoff distance and the potential function. For now, the elastic network model potential is the one that is available. In the output, each mode is represented by a slider. The user can visualize the motion of each mode independently by moving its corresponding slider manually or by checking its checkbox and then pressing on the play button. Also, the user can visualize the motion of a combination of modes selecting them before playing the motion. The transformations used in this motion can be set to linear or nonlinear and the amplitude of the motion can be increased/decreased by changing the scaling factor. During this motion, the user can activate a real time minimization using one of the provided algorithms (steepest descent, conjugated gradient or LBGFS) and defined values of minimization steps and minimization tolerance.

Finally, the user can either save/export a given conformation of the structure or the entire displayed trajectory by going into the "Save Frames" tabulation of the SAMSON element.

Please visit the Computing non-linear normal modes of biomolecules tutorial.

0.6.2 : Update3: Bugs fixed :

• Going backward in the SAMSON history after normal modes has been computed. 0.6.4: Update4: Bugs fixed:
• Minimum selected residues