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Index of Script Commands

Click on an individual command in the list to go to its documentation. Click on the package link at the beginning of each list to get a general overview of all commands in that package.

Table of contents:

Run

  • get_step - Gets the current time step
  • run - Runs the simulation for a given number of time steps
  • run_upto - Runs the simulation up to a given time step number

Option

Initialize

Integrate

Update

Compute

  • compute.thermo - Compute thermodynamic properties of a group of particles

Analyze

  • analyze.imd - Sends simulation snapshots to VMD in real-time
  • analyze.log - Logs a number of calculated quantities to a file
  • analyze.msd - Calculates the mean-squared displacement of groups of particles and logs the values to a file

Dump

  • dump.dcd - Writes simulation snapshots in the DCD format
  • dump.mol2 - Writes a simulation snapshot in the MOL2 format
  • dump.pdb - Writes simulation snapshots in the PBD format
  • dump.bin - Writes simulation snapshots in a binary format
  • dump.xml - Writes simulation snapshots in the HOOMD XML format

Potentials

Pair potentials

Many-body potentials

Bond potentials

Angle potentials

Dihedral potentials

Improper potentials

Electrostatic potentials

  • charge.pppm - Long-range electrostatics computed with the PPPM method

Wall potentials

  • wall.lj - Lennard-Jones wall force

Constraint forces

External forces

Other forces

Helpers

Group

Variants

Miscellaneous commands

Tune

  • tune.r_buff() - Make a series of short runs to determine the fastest performing r_buff setting

Benchmark

  • benchmark.series - Perform a series of short runs to benchmark overall simulation performance

Communication helpers