Description:
-Treat one or more sets of atoms as an independent rigid body. This +
Treat one or more sets of atoms as independent rigid bodies. This means that each timestep the total force and torque on each rigid body -is computed and the coordinates and velocities of the atoms in each -body are updated so that they move as a rigid body. This can be -useful for freezing one or more portions of a large biomolecule, or -for simulating a system of colloidal particles. +is computed as the sum of the forces and torques on its constituent +particles and the coordinates, velocities, and orientations of the +atoms in each body are updated so that the body moves and rotates as a +single entity.
-IMPORTANT NOTE: This fix is overkill if you just want to hold group of
-atoms stationary of have them move with a constant velocity. A
-simpler way to hold atoms stationary is to not include those atoms in
-your time integration fix. E.g. use "fix 1 mobile nve" instead of
-"fix 1 all nve", where "mobile" is the group of atoms that you want to
-move. You can move atoms with a constant velocity by assigning them
-an initial velocity (via the velocity command),
-setting the force on them to 0.0 (via the fix
+ Examples of large rigid bodies are a large colloidal particle, or
+portions of a large biomolecule such as a protein.
+ Example of small rigid bodies are patchy nanoparticles, such as those
+modeled by the Glotzer group, clumps of granular particles,
+lipid molecules consiting of one or more point dipoles connected to
+other spheroids or ellipsoids, and coarse-grain models of nano or
+colloidal particles consisting of a small number of constituent
+particles. Note that the fix shake command can also be
+used to rigidify small molecules of 2, 3, or 4 atoms, e.g. water
+molecules. That fix treats the constituent atoms as point masses.
+ The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheroids
+and ellipsoids. See the shape command and atom_style
+granular for more details on these kinds of
+particles. Finite-size particles contribute differently to the moment
+of inertia of a rigid body than do point particles. Finite-size
+particles can also experience torque (e.g. due to frictional granular
+interactions) and have an orientation. These
+contributions are accounted for by the fix.
+ Forces between particles within a body do not contribute to the
+external force or torque on the body. Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body. The neigh_modify
+exclude and delete_bonds
+commands are used to do this. For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
+ IMPORTANT NOTE: This fix is overkill if you simply want to hold a
+collection of atoms stationary or have them move with a constant
+velocity. A simpler way to hold atoms stationary is to not include
+those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
+instead of "fix 1 all nve", where "mobile" is the group of atoms that
+you want to move. You can move atoms with a constant velocity by
+assigning them an initial velocity (via the velocity
+command), setting the force on them to 0.0 (via the fix
setforce command), and integrating them as usual
(e.g. via the fix nve command).
Each body must have two or more atoms. An atom can belong to at most one rigid body. Which atoms are in which bodies can be defined via several options. @@ -214,4 +247,10 @@ exclude
The option defaults are force * on on on and torque * on on on meaning all rigid bodies are acted on by center-of-mass force and torque.
+(Zhang) Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). +