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### compute gyration/molecule command

Syntax:

    compute ID group-ID gyration/molecule

- ID, group-ID are documented in compute command
- gyration/molecule = style name of this compute command

Examples:

    compute 1 molecule gyration/molecule

Description:

Define a computation that calculates the radius of gyration Rg of individual molecules. The calculation includes all effects due to atoms passing thru periodic boundaries.

Rg is a measure of the size of a molecule, and is computed by this formula

where M is the total mass of the molecule, Rcm is the center-of-mass position of the molecule, and the sum is over all atoms in the molecule and in the group.

Rg for a particular molecule is only computed if one or more of its atoms are in the specified group. Normally all atoms in the molecule should be in the group, however this is not required. LAMMPS will warn you if this is not the case. Only atoms in the group contribute to the Rg calculation for the molecule.

Let Nmolecules be the number of molecules for which Rg is calculated. If not all molecules have atoms in the group, then the molecule with the lowest ID is the first of the Nmolecules. The next lowest ID is the second, etc, up to Nmolecules.

IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. See the dump custom command for a discussion of "unwrapped" coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.

Output info:

This compute calculates a global vector of Rg values where the length of the vector = Nmolecules. These values can be used by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.

The vector values calculated by this compute are "intensive". The vector values will be in distance units.

Restrictions: none

Related commands: none

compute gyration

Default: none