Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends i...

Instantaneous normal mode analysis of orientational motions in liquid water: Local structural effects We present an instantaneous-normal-mode analysis of liquid water at room temperature based on a computer simulated set of liquid configurations and we compare the results to analogous inherent-structure calculations. The separate translational and rotational contributions to each instantaneous ...

We use the instantaneous normal mode approach to provide a description of the local curvature of the potential energy surface of a model for water. We focus on the region of the phase diagram in which the dynamics may be described by mode-coupling theory. We find that the diffusion constant depends on the fraction of directions in configuration space connecting different local minima, supportin...