cg_openmm.simulation.rep_exch

Functions

extract_trajectory(topology, reporter[, ...])	Internal function for extract trajectory (replica or state) from .nc file, Based on YANK extract_trajectory code.
get_minimum_energy_ensemble(topology, ...[, ...])	Get an ensemble of low (potential) energy poses, and write the lowest energy structure to a PDB file if a file_name is provided.
make_replica_dcd_files(topology[, timestep, ...])	Make dcd files from replica exchange simulation trajectory data.
make_replica_pdb_files(topology[, ...])	Make pdb files from replica exchange simulation trajectory data.
make_state_dcd_files(topology[, timestep, ...])	Make dcd files by state from replica exchange simulation trajectory data.
make_state_pdb_files(topology[, output_dir, ...])	Make pdb files by state from replica exchange simulation trajectory data.
plot_replica_exchange_energies(...[, ...])	Plot the potential energies for a batch of replica exchange trajectories
plot_replica_exchange_energy_histograms(...)	Plot the potential energies for a batch of replica exchange trajectories
plot_replica_exchange_summary(...[, ...])	Plot the thermodynamic state assignments for individual temperature replicas as a function of the simulation time, in order to obtain a visual summary of the replica exchanges from a OpenMM simulation.
plot_replica_state_matrix(replica_state_indices)
process_replica_exchange_data([output_data, ...])	Read replica exchange simulation data, detect equilibrium and decorrelation time, and plot replica exchange results.
restart_replica_exchange(total_simulation_time)	Restart an OpenMMTools replica exchange simulation using an OpenMM coarse grained model and output .nc files from the previous segment of the simulation.
run_replica_exchange(topology, system, positions)	Run a OpenMMTools replica exchange simulation using an OpenMM coarse grained model.