GitLab

Allow specification of extra particles in PDB files via element field and extraParticleIdentifier

Loading a checkpoint marks that positions have been set

Record force group for AMOEBA forces

Improvements to addHydrogens()

Fixed a bug in serializing CustomCentroidBondForce

AMOEBA extrapolated polarization

More acos protections in Amoeba

Remove Jenkins badges from README.md

errors.

This copies the fix for the AmoebaTorsionTorsionForce over to the other two
forces that calculate angles via the inverse cosine -- specifically the in-plane
angle force and the stretch-bend force.  The TorsionTorsion fix did not
completely solve the occasional simulation blowup, although it did make it a
*lot* less frequent (it went from happening within 5 minutes to happening ~once
per day).

Fix push of dev user and developer guide HTMLs to S3

Also build the HTML user guide in travis

Document how to turn on API docs building

Add hooks for parameterizing unmatched residues in ForceField

AmoebaTorsionTorsionForce avoids singularity in acos()