Fix v-site positions not set by OpenMM

[SimonBoothroyd]

Description

This PR fixes a bug whereby the positions of v-sites aren't correctly added to arrays of atom positions prior to being set on an OMM context.

Notes

• Currently we enforce that v-sites must be at the end of the system, same as the OpenFF TK, to simplify the position logic.

Status

• [X] Ready to go

[codecov[bot]]

Codecov Report

Merging #389 (abd6ff8) into master (3c0d16a) will increase coverage by 0.02%. The diff coverage is 96.77%.