Neighbor Lists

Collective variables that can be speed up making us of neighbor lists:

• COORDINATION
• DHENERGY
• PATHMSD

By tuning the cut-off for the neighbor list and the frequency for the recalculation of the list it is possible to balance between accuracy and performances.

Notice that for COORDINATION and DHENERGY using a neighbor list could imply that a smaller number of atoms are requested to the host MD engine. This is typically true when considering COORDINATION of a small number of atoms (e.g. a ligand) again many atoms (e.g. water). When the neighbor list is used, only the water atoms close to the ligand will be requested at each step.