ParallelTemperingSampler

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Daniel Konstantinovsky
Posts: 77
Joined: Tue Jun 11, 2019 12:21 pm

ParallelTemperingSampler

Post by Daniel Konstantinovsky » 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!
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Peter Eastman
Posts: 2544
Joined: Thu Aug 09, 2007 1:25 pm

Re: ParallelTemperingSampler

Post by Peter Eastman » Fri Dec 11, 2020 10:30 am

I don't think any of the openmmtools developers monitor this forum. You might have more success opening an issue at https://github.com/choderalab/openmmtools.

MDTraj should be able to convert netCDF to DCD.
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