Molecular dynamics workflow
Plan input preparation, equilibration, production and analysis for a CEMP AutoCompute MD workflow.
Prepare a compatible system
Choose the MD workflow and record components, counts, charges, force-field assumptions and boundary conditions. Use the current workflow template and review the generated topology.
Separate simulation stages
Energy minimization and equilibration prepare the system. Inspect density, temperature and other relevant quantities before interpreting production. Choose the integration step and output interval with the intended analysis in mind.
Keep the simulation conditions
Retain the topology, simulation parameters and outputs. Transport estimates require a defined time window, units and checks that the trajectory is long enough for the analysis.