cg_openmm.simulation.tools

Functions

build_mm_simulation(topology, system, positions)	Build an OpenMM Simulation()
get_mm_energy(topology, system, positions)	Get the OpenMM potential energy for a system, given a topology and set of positions.
minimize_structure(cgmodel, positions[, ...])	Minimize the potential energy
plot_simulation_data(simulation_times, y_data)	Plot simulation data.
plot_simulation_results(...)	Plot all data from an OpenMM output file
read_simulation_data(simulation_data_file, ...)	Read OpenMM simulation data
run_simulation(cgmodel, ...[, friction, ...])	Run OpenMM() simulation