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if I've understood this right, there's fields that you can set that do nothing in an MD protocol; which is confusing but not harmful.
I think the fix for this can be to deprecate the IntegratorSettings usage in MDProtocol in favour of the correct fields, with appropriate warnings etc, but it can be done in 1.x
Looking at the IntegratorSettings,
reassign_velocities
,n_restart_attempts
, andconstraint_tolerance
, don't get used in the PlainMDProtocol.This is because the PlainMDProtocol uses a LangevinMiddleIntegrator, whilst the RFE and AFE Protocols use LangevinDynamicsMove.
The difference in use of integrators is expected, but the different classes should really be used to avoid user confusion.
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