Users.Programs.mol_Vibrations

mol_Vibrations: Normal mode analysis of molecular vibrations

Starting from a given (typically a minimum energy) configuration, the MATLAB function mol_Vibrations.m numerically calculates the Hessian (matrix of 2nd derivatives) of the potential energy hypersurface (force field) of a molecular system and diagonalizes it. The vibrational normal mode frequencies are obtained as square roots of the eigenvalues. The displacements defining the normal mode coordinates are contained in the corresponding eigenvectors.

Source code

The MATLAB function mol_Vibrations.m can be found here

File I/O

The initial optimized geometries is read from the head of an xyz-file named sorted...xyz. If desired, displacements of the atomic positions can be written to files vib_movie...xyz (one file for each normal mode). These results can be visualized (e.g. using JMOL or VMD software). If desired, also scans of the force field energy along these coordinates can be generated and written to files vib_scan...xyz.

Variables

Note that function mol_Initialize.m has to be run previously in order to initialize all variables in use. Of particular interest are the following structures:

• molecule
• simulation
• initial
• intra
• inter
• vibrations