Fix inconsistent units from get_box and nonbondedCutoff #6
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…that were used to set it up
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Fixed issues with testing and removed draft status. Will be merged pending linting passing. Thanks for the PR @rkingsbury! |
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Thanks @orionarcher ! This is sufficiently important to get right that I think some follow up work is warranted - e.g. adding a more comprehensive test to confirm that we get the expected density in the expected units (as per the TODO item you added). I will open an issue related to that so we don't lose track. |
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The
nonbondedCutoffin OpenMM must be specified in units of nm, howeverget_box(which is used byparameterize_system) returns box dimensions in angstrom. The subsequent calculation at this line thus incorrectly sets thenonbondedCutoffto either 10 nm (100 Angstrom), or 10x the intended box size.This PR contains a fix for the inconsistent units, calculating the
nonbondedCutoffas the min of (1 nm) or (1/2 the box size in nm). I still need to add a test.