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rename equil_torsion_angle everywhere #104

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cwalker7 opened this issue Dec 2, 2020 · 2 comments
Closed

rename equil_torsion_angle everywhere #104

cwalker7 opened this issue Dec 2, 2020 · 2 comments
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For release This needs to be addressed before first code release

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@cwalker7
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cwalker7 commented Dec 2, 2020

The parameter we have been calling 'equil_torsion_angle' is actually the phase offset of periodic torsions. http://docs.openmm.org/development/api-python/generated/simtk.openmm.openmm.PeriodicTorsionForce.html

It seems misleading to keep that variable name, so we should rename it something else like 'torsion_phase_offset'.

This is why we were seeing a torsion peak at 180-equil_torsion_angle for periodicity=1. (see shirtsgroup/analyze_foldamers#12)
@cwalker7 cwalker7 added the For release This needs to be addressed before first code release label Dec 2, 2020
@mrshirts
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mrshirts commented Dec 2, 2020

Yeah, go ahead and make the change (just make sure that examples are updated as well).

@cwalker7
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cwalker7 commented Dec 7, 2020

Ok I changed this here: #102

@cwalker7 cwalker7 closed this as completed Dec 7, 2020
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@mrshirts @cwalker7