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Introduction
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14 Molecular Dynamics
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Molecular Dynamics (MD) in ICM uses the functions in OpenMM - if you use this feature please cite OpenMM.

To run an MD simulations:

  • Convert your protein to an ICM object.
  • MolMechanics/Run MD Simulation
  • Use the drop down box to select the protein.
  • Select whether or not you wish to solvate the protein.
  • Select the length of time for the simulation in ns.
  • Click OK.

To add restraints:

  • Make a copy of the protein you wish to simulate - right click on the name of the protein in the ICM workspace (left hand side) and choose the option 'clone'.
  • Select the region of the cloned molecule you wish to restrain and convert that selection to an 'orange' selection as described here.
  • Go to MolMechaics/Run MD Simulation as described above and choose the selection in the Restrain dialog box.
  • Click OK to run the simulation.


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