Section: New Results

NOLB nonlinear normal modes

Participants : Alexandre Hoffmann, Sergei Grudinin.

We developed a new conceptually simple and computationally efficient method for nonlinear normal mode analysis called NOLB [4]. This is a logical evolution of the RTB-subspace method developed by Y.-H. Sanejouand and colleagues [38], [80]. We demonstrated how to physically interpret the eigenvalues computed in the RTB basis in terms of angular and linear velocities applied to the rigid blocks and how to construct a nonlinear extrapolation of motion out of these velocities. The key observation of our method is that the angular velocity of a rigid block can be interpreted as the result of an implicit force, such that the motion of the rigid block can be considered as a pure rotation about a certain center.

Overall, our method produces better structures compared to the standard approach, especially at large deformation amplitudes, as we demonstrate by visual inspection, energy and topology analyses, and also by the MolProbity service validation. Also, our method is scalable and can be applied to very large molecular systems, such as ribosomes.

Standalone executables of the NOLB normal mode analysis method are available at https://team.inria.fr/nano-d/software/nolb-normal-modes/. A graphical user interface created for the SAMSON software platform will be made available at https://www.samson-connect.net.