Simulation ProceduresΒΆ
Since moving the particles changes the distances between them and thus their forces, molecular dynamics involves continuously integrating these equations of motion to obtain trajectories numerically. This leads to the overall scheme for MD simulations, shown in the diagram below and consisting of the following stages:
- Set up initial system - obtain initial positions and velocities of atoms
- Calculate atomic forces based on potential model
- Calculate particle motion from force integration
- Calculate physical properties - collect instantaneous data for statistical purposes
- Repeat until done
Note
In DL_POLY, system trajectories can be saved into a file called HISTORY. To do this, the directive traj must be included in the CONTROL file. For example, to save the positions and velocities of the system at every 100 MD steps (not timestep!):
traj 0 100 1
This will produce a time series of atomic ocnfigurations. The time interval between the configurations would be simply multiply of the MD timstep.