groups file contains information about how atoms should be grouped together. The concept of "group" in DoSPT is related to the concept of molecule in chemistry. The desired characteristics of a "group" of atoms are 1) well-defined center of mass, 2) well defined symmetry number, 3) the number and identity of the atoms that form the group does not change during the MD run. These conditions are satisfied in usual classical-MD simulations, where bonds cannot be broken or created. In ab initio MD, it is possible that such events will happen, and one should proceed with caution. For instance, when modeling a solvated proton in liquid water, the H+ ion is highly mobile and will constantly switch between neighboring water molecules. In such a situation, groups are "created" and "annihilated" during the MD run. This situation can be handled making use of the topology file. The topology page further discusses this issue.
groups file has the following structure:
natoms ngroups n1 s1 n1_1 n1_2 n1_3 ... n2 s2 n2_1 n2_2 n2_3 ... ...
s1 are the number of atoms and symmetry number of group 1, respectively.
n1_2, etc. are the indices of all the atoms which belong to group 1, that is, the order in which they appear in the trajectory file.
groups files are rarely constructed by hand (unless you enjoy repetitive and error-prone tasks), and are usually built using some scripting language such as Python or bash (see Tutorial 1 for a Python example). The topology feature can correct for defective
groups files according to bonding and grouping information provided by the user. This feature might be the only choice to carry out a reasonable simulation when bond breaking exists. However, currently one needs to provide an initial
groups file, even if the topology feature will completely regroup the atoms. We recognize that this is somewhat inconvenient and will strive to provide a fully automatic group-building capability in the near future.