gonzalezma
commented
8 months ago I would say this is the correct TIP4P geometry. The important point is that the 4th position is assigned to a dummy or special atom, and not to an oxygen atom. But it should be retained as it could be needed to e.g. compute the molecular dipole moment.
Description of the error Converting certain dlpoly files leads to a MDANSE trajectory file incorrect atoms. Converting the water with velocities from MDANSE-Examples can lead to a trajectory with waters that have two oxygens. For this case the issue occurs because it incorrectly assigns the point charge on tip4p to a oxygen atom.
Describe the expected result A trajectory of waters with the correct number of atoms.
Additional details This occurs in both the old and new versions of MDANSE.