\(\renewcommand{\AA}{\text{Å}}\)

fix recenter command

Syntax

fix ID group-ID recenter x y z keyword value ...

  • ID, group-ID are documented in fix command

  • recenter = style name of this fix command

  • x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)

  • zero or more keyword/value pairs may be appended

  • keyword = shift or units

    shift value = group-ID
  group-ID = group of atoms whose coords are shifted
units value = box or lattice or fraction

Examples

fix 1 all recenter 0.0 0.5 0.0
fix 1 all recenter INIT INIT NULL
fix 1 all recenter INIT 0.0 0.0 units box

Description

Constrain the center-of-mass position of a group of atoms by adjusting the coordinates of the atoms every timestep. This is simply a small shift that does not alter the dynamics of the system or change the relative coordinates of any pair of atoms in the group. This can be used to ensure the entire collection of atoms (or a portion of them) do not drift during the simulation due to random perturbations (e.g. fix langevin thermostatting).

Distance units for the x,y,z values are determined by the setting of the units keyword, as discussed below. One or more x,y,z values can also be specified as NULL, which means exclude that dimension from this operation. Or it can be specified as INIT which means to constrain the center-of-mass to its initial value at the beginning of the run.

The center-of-mass (COM) is computed for the group specified by the fix. If the current COM is different than the specified x,y,z, then a group of atoms has their coordinates shifted by the difference. By default the shifted group is also the group specified by the fix. A different group can be shifted by using the shift keyword. For example, the COM could be computed on a protein to keep it in the center of the simulation box. But the entire system (protein + water) could be shifted.

If the units keyword is set to box, then the distance units of x,y,z are defined by the units command - e.g. Angstroms for real units. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. A fraction value means a fractional distance between the lo/hi box boundaries, e.g. 0.5 = middle of the box. The default is to use lattice units.

Note that the velocity command can be used to create velocities with zero aggregate linear and/or angular momentum.

Note

This fix performs its operations at the same point in the timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt. Thus fix recenter should normally be the last such fix specified in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way.

Note

If you use this fix on a small group of atoms (e.g. a molecule in solvent) without using the shift keyword to adjust the positions of all atoms in the system, then the results can be unpredictable. For example, if the molecule is pushed consistently in one direction by a flowing solvent, its velocity will increase. But its coordinates will be re-centered, meaning it is moved back towards the force. Thus over time, the velocity and effective temperature of the molecule could become very large, though it won’t actually be moving due to the re-centering. If you are thermostatting the entire system, then the solvent would be cooled to compensate. A better solution for this simulation scenario is to use the fix spring command to tether the molecule in place.

Restart, fix_modify, output, run start/stop, minimize info

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

This fix computes a global scalar which can be accessed by various output commands. The scalar is the distance the group is moved by fix recenter.

This fix also computes global 3-vector which can be accessed by various output commands. The 3 quantities in the vector are xyz components of displacement applied to the group of atoms by the fix.

The scalar and vector values calculated by this fix are “extensive”.

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

This fix should not be used with an x,y,z setting that causes a large shift in the system on the first timestep, due to the requested COM being very different from the initial COM. This could cause atoms to be lost, especially in parallel. Instead, use the displace_atoms command, which can be used to move atoms a large distance.

Default

The option defaults are shift = fix group-ID, and units = lattice.