Automatically reduce the tadfactor to 4 when fully flexible segments are defined

[amjjbonvin]

• Tests added for the new code
• Documentation added for the code changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Solves issue #1000.
In the flexref module, the tad factor defining the time step for an MD integrations step is now automatically reduced from the default of 8 to 4 for the high temperature initial stage of the simulated annealing protocol. This will reduce possible job failures (models crashing) in the flexref module.

Integration test will be added once the integration-tests branch is merged.

[VGPReys]

This overwrites any user defined values of this tadfactor parameter?
Or it applies only at high temperatures ?

[amjjbonvin]

This overwrites any user defined values of this tadfactor parameter? Or it applies only at high temperatures ?

In the current implementation it will take the minimum value of the user-defined value and 4 for the high temperature stage only. For the last two stages with flexible side-chains and backbone the value was already set to 1