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14 Molecular Dynamics

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

To run an MD simulations using Amber force field ff14SB:

  • 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.


The conformation snapshots are stored at regular time intervals during the MD simulation and are embedded in the ICM object as a stack.

Results Analysis:

Right click on the stack of MD snapshots in the ICM workspace and choose Stack Calculations. In this dialog box you can analyze

  • Distance changes between snapshots.
  • RMSD to Reference - Read in a separate object as a reference and make the selection you want to analyze. You can choose to analyze the structures 'static' or superimpose. A table and plot of the RMSDs are displayed. This is a useful tool for analysis of a Molecular Dynamics run. Your x-axis will be the time in ns / number of conformations so if you chose 1ns and 50 conformations (snapshots) then each point is 1ns/50 = 0.02 ns
  • Torsion Changes - Select a pair of atoms on a rotatable bond to calculate the torsion angle.
  • Area Changes - use green and orange selections to calculate differences in area
  • RTCNN - use green and orange selections for receptor/ligand respectively to calculate RTCNN docking score.
  • ClusterTree - make a selection of atoms to compare and then a cluster tree will be displayed. You can then 'select-tree{select} a diverse set of conformations in the tree.

RIDE GPU Benchmark

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