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I've made sure that sigma is not set to 0 for any LJ parameters or exceptions.
I've added some unit tests for this based on serialising the OpenMM context to XML.
I have also checked that the
include_constrained_energies
option works, and added documentation about this plus a unit test.This pull request fixes an externally reported issue.
devel
into this branch before issuing this pull request (e.g. by runninggit pull origin devel
): [y]Suggested reviewers:
@lohedges