The group concept#

The GROMACS MD and analysis programs use user-defined groups of atoms to perform certain actions on. The maximum number of groups is 256, but each atom can only belong to six different groups, one each of the following:

temperature-coupling group

The temperature coupling parameters (reference temperature, time constant, number of degrees of freedom, see The leap-frog integrator) can be defined for each T-coupling group separately. For example, in a solvated macromolecule the solvent (that tends to generate more heating by force and integration errors) can be coupled with a shorter time constant to a bath than is a macromolecule, or a surface can be kept cooler than an adsorbing molecule. Many different T-coupling groups may be defined. See also center of mass groups below.

freeze group

Atoms that belong to a freeze group are kept stationary in the dynamics. This is useful during equilibration, e.g. to avoid badly placed solvent molecules giving unreasonable kicks to protein atoms, although the same effect can also be obtained by putting a restraining potential on the atoms that must be protected. The freeze option can be used, if desired, on just one or two coordinates of an atom, thereby freezing the atoms in a plane or on a line. When an atom is partially frozen, constraints will still be able to move it, even in a frozen direction. A fully frozen atom can not be moved by constraints. Many freeze groups can be defined. Frozen coordinates are unaffected by pressure scaling; in some cases this can produce unwanted results, particularly when constraints are also used (in this case you will get very large pressures). Accordingly, it is recommended to avoid combining freeze groups with constraints and pressure coupling. For the sake of equilibration it could suffice to start with freezing in a constant volume simulation, and afterward use position restraints in conjunction with constant pressure.

accelerate group

On each atom in an “accelerate group” an acceleration \(\mathbf{a}^g\) is imposed. This is equivalent to a mass-weighted external force. This feature makes it possible to drive the system into a non-equilibrium state to compute, for example, transport properties.

energy-monitor group

Mutual interactions between all energy-monitor groups are compiled during the simulation. This is done separately for Lennard-Jones and Coulomb terms. In principle up to 256 groups could be defined, but that would lead to 256\(\times\)256 items! Better use this concept sparingly.

All non-bonded interactions between pairs of energy-monitor groups can be excluded (see details in the User Guide). Pairs of particles from excluded pairs of energy-monitor groups are not put into the pair list. This can result in a significant speedup for simulations where interactions within or between parts of the system are not required.

center of mass group

In GROMACS, the center of mass (COM) motion can be removed, for either the complete system or for groups of atoms. The latter is useful, e.g. for systems where there is limited friction (e.g. gas systems) to prevent center of mass motion to occur. It makes sense to use the same groups for temperature coupling and center of mass motion removal.

Compressed position output group

In order to further reduce the size of the compressed trajectory file (xtc or tng), it is possible to store only a subset of all particles. All x-compression groups that are specified are saved, the rest are not. If no such groups are specified, than all atoms are saved to the compressed trajectory file.

The use of groups in GROMACS tools is described in sec. Using Groups.