Users.Programs.mol_Dynamics

mol_Dynamics.m: Molecular dynamics simulations

Starting from a given configuration (in many but not in all cases a minimum energy configuration), the MATLAB function mol_Dynamics.m propagates the molecular system according to Newton's equations of motion (Langevin and/or Smoluchowski should follow soon), thereby generating a trajectory with (hopefully!) constant energy (sampling an NVE ensemble). Alternatively, a simulation for constant temperature (sampling an NVT ensemble) can be run by using a numerical "thermostat". Implementation of a "barostat" (sampling an NPT ensemble) for simulations at constant pressure coming soon ...

Source code

• The MATLAB function mol_Dynamics.m

• Analysis of MD data

• Graphs of MD data

• Saving MD data

File I/O

The initial minimum energy geometry is either constructed from model functions or it will beread 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

Generation of initial conditions

• Velocity distribution for constant E

• Velocity distribution for constant T

Propagators

• For a list of implemented algorithms, see here

Thermostats

• For a list of implemented algorithms, see here