search

choderalab / protons

OpenMM testbed for constant-pH methodologies.
http://protons.readthedocs.io/
MIT License
20 stars 13 forks source link

Add analysis module #109

Closed bas-rustenburg closed 7 years ago

bas-rustenburg commented 7 years ago

This PR adds the BAR analysis and other related plotting tools to perform diagnostics and analyze results of protons simulations that use the netCDF reporter file formats.

Note that tests depending on the netCDF format have a tendency to segfault on linux, so they're not reliable enough to run on travis. I've verified that they pass locally, and this behavior has not been observed outside of the testing framework.

bas-rustenburg commented 7 years ago

Still seeing strange segmentation faults, now in code that isn't related to netCDF. Tests pass on the cluster. I'm going ahead with merging this.

jchodera commented 7 years ago

See @Lnaden and the #yank channel on slack for info on how to work around the segfault by moving the openmm dev package tests to a separate optional travis branch and using release openmm for standard py27/35/36 tests.

Lnaden commented 7 years ago

More specifically, look at choderalab/openmmtools#275

bas-rustenburg commented 7 years ago

Ah. Thanks, that is helpful.