Topology sanity checklist

mosdef-hub / gmso

Flexible storage of chemical topology for molecular simulation

https://gmso.mosdef.org

MIT License

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Topology sanity checklist #105

Open ahy3nz opened 5 years ago

ahy3nz commented 5 years ago

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 commented 5 years ago

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 #85 )

mattwthompson commented 5 years ago

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 ?)