Users.Programs.mol_SortMinima

mol_SortMinima: Sort minimum energy conformations

After having run function mol_Optimize.m one or more times, the MATLAB function mol_SortMinima can be used to sort the generated minima. The lowest energy conformations go first, so that there is some chance to find the global minimum in the head of the file.

Source code

The MATLAB function mol_SortMinima.m can be found here

File I/O

The unsorted minimum energy geometries are read from an xyz-file named minima...xyz. The sorted output is written to a data file named sorted...xyz. This can be visualized (e.g. using JMOL or VMD software).

Variables

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

• molecule
• simulation
• intra
• inter