search

choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
http://openmmtools.readthedocs.io
MIT License
252 stars 81 forks source link

[Question] How do I inspect the trajectories saved by MultiStateReporter? #717

Open mkrompiec opened 1 year ago

mkrompiec commented 1 year ago

How do I visualise trajectories saved by MultiStateReporter? I'm playing with the OpenFE demo, which generates "simulation.nc" and "checkpoint.nc", via MultiStateReporter.

mkrompiec commented 1 year ago

Is it related to https://github.com/choderalab/perses-barnase-barstar-paper/blob/main/scripts/05_analyze/run_make_traj_per_replica.py and https://github.com/choderalab/openmmtools/issues/678 ?

ijpulidos commented 1 year ago

@mkrompiec Thanks for your interest in the tools in our ecosystem! It is indeed related to both of those things. We have been lacking on this front for a while, but this is indeed on our roadmap and soon we will be putting the effort to make this easier to do and more integrated in our API. In the meantime, feel free to report any issues with the referenced scripts or API points or bring up specific questions about them. We will try our best to solve them, as possible.

mkrompiec commented 1 year ago

Thank you!