Topology sanity checklist

[ahy3nz]

Keeping a running list of sanity checks for molecular simulation

• Charge neutrality
• Overly-long bonds (will need MIC information)
• Rigid bonds that aren't at their equilibrium bond length
• All bonds, angles, dihedrals, etc. have parameters

Anyone is welcome to post things that would be good sanity checks

[ahy3nz]

• If 2 Bonds are "adjacent", then there should be an associated Angle (but for drude oscillators, while a bond is defined for the drude particle, there should be no angles involving the drude) (see discussion in this PR Topology update calls #85 )

[mattwthompson]

For the above case, that should be fine as long as we have a different class for the connection that ties drude oscillators to their parent atoms (Spring ?)