- meld.helpers.setup_replica_exchange(system, n_replicas, n_steps, n_trials=None, adaptation_growth_factor=2.0, adaptation_burn_in=50, adaptation_adapt_every=50, adaptation_stop_after=None, adaptation_min_acc_prob=0.02, mpi_timeout=60000)
Setup replica exchange
ISystem) – The system to be simulated
int) – The number of replicas to be simulated
int) – The number of steps of replica exchange to run
int]) – The number of trials to run per exchange
float) – The growth factor for adaptation
int) – The number of steps to ignore after adapting
int) – The number of steps to run between adaptation
int]) – The number of steps to run before stopping adaptation
float) – The minimum acceptance probability when adapting
int) – The number of seconds to wait for MPI communication to complete
Replica exchange adaptation works as follows. First adaptation_burn_in steps are run and no statistics about exchange are collected. Then adaptation_adapt_every steps are run and the average acceptance rate is calculated. Any acceptance rates below adaptation_min_acc_prob are clamped at the minimum. Then adaptation is performed to equalize the acceptance rates. After each adaptation, the values of adaptation_burn_in and adaptation_adapt_every are multiplied by adaptation_growth_factor.
If n_trials is None, then the number of trials is n_replicas**2.
- Return type