AtomicSystem.remove_atoms

AtomicSystem.remove_atoms(indices)

Remove specified atoms from the system and update topology accordingly.

Parameters:

indicesSequence[int] or int

Index or sequence of indices of the atoms to remove.

Notes

This method automatically reindexes the remaining atoms, updates velocities, removes unused atom types from internal mass and charge storage, and updates or removes any bonds, angles, dihedrals, or impropers containing the removed atoms.