IntegratorSettings don't all apply to the MD Protocol

[IAlibay]

Looking at the IntegratorSettings, reassign_velocities, n_restart_attempts, and constraint_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.

[mikemhenry]

perhaps we could add warnings if they are set in the protocol/"this setting isn't used by the protocol and will be removed in the future"

[richardjgowers]

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

[jameseastwood]

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