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choderalab / protons

OpenMM testbed for constant-pH methodologies.
http://protons.readthedocs.io/
MIT License
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Ions are accumulating over the course of several NCMC protocols #124

Closed bas-rustenburg closed 5 years ago

bas-rustenburg commented 6 years ago

There seems to be accumulation of ions over the course of a simulation.

bokeh_plot

I thought I had built ways to prevent this. I tested the selection of salt here: https://github.com/choderalab/protons/blob/master/protons/tests/test_explicit.py#L733

So perhaps I overlooked something, or something is wrong inside of the NCMCProtonDrive.

bas-rustenburg commented 5 years ago

This was fixed by #126.