Syntax:
compute ID group-ID gyration/molecule
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.
The ordering of per-molecule quantities produced by this compute is consistent with the ordering produced by other compute commands that generate per-molecule datums. Conceptually, them molecule IDs will be in ascending order for any molecule with one or more of its atoms in the specified group.
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
Default: none