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.

Warning

Notice that the calculation of the neighbor list is not not parallelized for COORDINATION and DHENERGY. As a consequence, if you run with many processors and/or OpenMP threads, the neighbor list might even make the calculation slower.