Tutorial 6.3: Setting the Time Step
The time step in an MD simulation should be as large as possible, to allow the simulation to cover physically interesting time scales, without sacrificing accuracy. In this tutorial, you will examine how the size of the time step affects an MD simulation on the harmonic oscillator.
Create a new folder for your work on this tutorial.
If you have NOT completed Tutorial 1 (MD Simulation on the Harmonic Oscillator), you need to download the following files:
PDB File: N2_w_fixed_atom.pdb
FF Mod File: harmonic_oscillator.frcmod
Recipe...: harmonic_oscillator recipe.json
INSTRUCTIONS (brief version):
Run a series of simulations identical to those of Tutorial 1, using timesteps of 0.1 fs, 0.3 fs, 1 fs (done in Tutorial 1), 3 fs, 10 fs, 30 fs... In each case run the trajectory for a total of 1 ps (1000 fs), so you can compare the results directly with those of Tutorial 1.
1. When the time step gets too large, the simulation will "blow up" -- become unstable. Determine the maximum time step that keeps the simulation for the full 1 ps trajectory.
2. The simulation should be more accurate for shorter time steps. Make a table showing the fractional fluctuation in total energy as a function of step size. (You determined the fractional fluctuation for a 1 fs time step in Tutorial 1.)
3. Write a brief summary that ties these results together.
INSTRUCTIONS (detailed version):
If you need detailed instructions for this tutorial, they can be found here.