Normal Mode Analysis

This logic performs a Normal Mode Analysisof the given 3d structure. It can be used to visualize basic molecular movement modes.

The logic has three modes that represent the three different major parts of NMA. In the first step the volume is filled with pseudo atoms. In the second step an elastic network is created with respect to the positions of the pseudo atoms. It is based on a Hessian Matrix and a cutoff distance. Last, eigenvector/eigenvalue decomposition is performed and in a last step they are applied on the pseudoatoms. The workflow is split into 3 separate parts to allow the user to check intermediate results.

Choose between the three different NMA-modes Fit Pseudo Atoms Into Volume, Compute Normal Modes or Apply Normal Modes.

Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences.