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Command: tug

tug  tugatoms  toAtoms  refatoms  [ steps  N ] [ frames  M ] [ errorTolerance  f ] [ forceConstant  c ] [ temperature  T ] [ cutoff  d ] [ platform  compute-platform ] [ finish  true | false ]

The tug command pulls the tugatoms to the positions of the refatoms while running molecular dynamics (MD) on the entire atomic model(s) containing the tugatoms. Atoms in any other models do not exert forces during the calculation; the positions of the refatoms are simply used as points toward which the tugatoms are pulled. If any refatoms are in the same model as any tugatoms, they will exert a force during MD, but only their initial positions will be used as target locations. The two specifications must contain equal numbers of atoms, which will be paired in the order given.

Atomic models containing any tugatoms must be parametrized in OpenMM (details...). Currently, this requires a fully protonated structure containing only standard residues and/or water. Protons can be added beforehand with the command addh. N steps of dynamics (default 50) are calculated for each of M graphics update frames (default 50) using a variable time-step Langevin integrator, with energy minimization occurring automatically if a maximum force is exceeded due to bad geometry. Default settings are an errorTolerance of 0.001, a forceConstant of 1000 N/m for pulling atoms to their target locations, temperature 100 K, and a nonbonded-interaction cutoff distance of 10.0 Å.

The platform option specifies which compute-platform should run the OpenMM calculation, with possibilities depending on the user's specific system:

If finish is true, the command does not return until all M frames are drawn; this is for use in scripts that require the MD to be finished before continuing. By default (finish false), subsequent commands are allowed to execute immediately.

Saving a session before using tug is advised, since the resulting changes in atomic positions cannot be reversed with undo or by restoring a previously saved view.

See also: build, Build Structure, mouse modes tug and minimize

UCSF Resource for Biocomputing, Visualization, and Informatics / February 2024