Frequently Asked Questions

There are no reactions

  • Increase the temperature

  • NanoReactor: Increase DiffusionTime, set MinVolumeFraction to a smaller value, set InitialRadius to a smaller value

  • LatticeDeformation: Set MinVolumeFraction to a smaller value, decrease Period

  • Set MolecularDynamics UseDeuterium=No

  • Ensure that you use a reactive potential (e.g. ReaxFF, DFTB, MLPotential)

Note: The best value for MinVolumeFraction depends on the initial density (MolecularDynamis%BuildSystem%Density). If you decrease the initial density, you may need to also decrease the MinVolumeFraction.

Tip

Run the simulation with the fast UFF force field to get a feeling for if the initial settings are reasonable. With UFF no reactions will happen but you can still see how the density fluctuates in the MD simulation.

There are too many reactions

  • Decrease the temperature

  • NanoReactor: Decrease DiffusionTime, set MinVolumeFraction to a larger value, set InitialRadius to a larger value

  • LatticeDeformation: Set MinVolumeFraction to a larger value, increase Period

  • Set MolecularDynamics UseDeuterium=Yes

Note: The best value for MinVolumeFraction depends on the initial density (MolecularDynamis%BuildSystem%Density). If you decrease the initial density, you may need to also decrease the MinVolumeFraction.

The MD simulations are too slow

  • Decrease the number of atoms

  • Decrease the number of NanoReactor or LatticeDeformation cycles

  • Increase the MD time step

How should I set the density and compression factor?

  • Nanoreactor: The density should be approximately the normal liquid density of your system, with a compression factor of about 0.5-0.7

  • Lattice deformation: The density should be about half the normal liquid density of your system, with a compression factor of about 0.15-0.30

The simulation explodes

  • Follow the steps for There are too many reactions.

  • Decrease the MD time step

How do I use computing resources efficiently?

The steps are parallelized as follows:

  • MolecularDynamics runs as many jobs in parallel as possible, respecting the allocation (NSCM)

  • NetworkExtraction runs NumSimulations ChemTraYzer2 jobs sequentially in serial; then NSCM geometry optimizations and single points are run in parallel.

  • ProductRanking runs in serial

Thus, most of the computational steps except ProductRanking are run efficiently in parallel. You may thus choose to set ProductRanking Enabled=False if you have a large node allocated, and then restart from the previous results using ProductRanking Enabled=True on a smaller allocation.