#21 Modify SCPISM to use Van der Waals in Atom

[Anonymous]

When we discovered the bug in GB, we realized that Van der Waal radii should be associated with Atoms, not AtomTypes. For the partial fix, we created a new field in the Atom and modified the GB code, OpenMM wrapper, and the TPR reader to use that new field. For non-TPR inputs, BuildTopology currently copies the value from the AtomType field to the Atom field. We have not removed the old field as SCPISM still depends on it. We need to correct BuildTopology to set the correct values for the Atom field, update SCPISM to use the new field, remove the old field, and rename the new field appropriately.