Users.Programs.mol_MonteCarlo

mol_MonteCarlo.m: Monte Carlo simulations

Starting from a given configuration (in many but not in all cases a minimum energy configuration), the MATLAB function mol_MonteCarlo.m generates a random walk sequence of conformations, which should - theoretically - be distributed according to a canonical NVT distribution. There are various strategies how to generate trial moves, see below.

As a variant, this code can also perform simulated annealing simulations, where a global minimum of the potential energy surface is searched by means of an MC simulation, in which the temperature is reduced slowly enough. This represents a promising alternative to the direct energy minimization algorithms implemented in the mol_Optimize code.

Source code

• The MATLAB function mol_MonteCarlo.m

• Analysis of MC data

• Graphs of MC data

• Saving MC data

File I/O

The initial minimum energy geometry is either constructed from model functions or it will be read from the head of an xyz-file. The time evolution of the atomic position can be written to an xyz-file named nve...xyz or nvt...xyz in certain time intervals. These results can be visualized as a movie (e.g. using JMOL or VMD software).

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
• dynamics

Algorithms

• For a list of implemented algorithms, see here