ParallelTemperingSampler
Posted: Thu Dec 10, 2020 7:04 pm
Hi!
I am trying to set up a temperature replica exchange simulation with openmmtools. The openmmtools documentation doesn't have much detail on the format of the netCDF output of the ParallelTemperingSampler class run method. How can I feed a trajectory reporter into ParallelTemperingSampler to get positions vs time and the frequency I want? Also, i pass my simulation object a reporter (reporter = MultiStateReporter(storage_path, checkpoint_interval=1)) but in the netCDF file the checkpoint interval is still set to 50, the default. How can I fix this as well? Finally, is there a utility to efficiently convert trajectory info in the netCDF to another binary format like DCD that other libraries prefer?
Thank you!
I am trying to set up a temperature replica exchange simulation with openmmtools. The openmmtools documentation doesn't have much detail on the format of the netCDF output of the ParallelTemperingSampler class run method. How can I feed a trajectory reporter into ParallelTemperingSampler to get positions vs time and the frequency I want? Also, i pass my simulation object a reporter (reporter = MultiStateReporter(storage_path, checkpoint_interval=1)) but in the netCDF file the checkpoint interval is still set to 50, the default. How can I fix this as well? Finally, is there a utility to efficiently convert trajectory info in the netCDF to another binary format like DCD that other libraries prefer?
Thank you!