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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.

ICM offers several key features for optimizing molecular dynamics (MD) simulations using OpenMM:

  • GPU Optimized Code: MD in ICM is designed to leverage GPU acceleration, enabling fast MD simulations. It can achieve performance speeds ranging from 3-12 picoseconds per second (ps/s) or 0.2-1.0 microseconds per day (us/day) on affordable workstations, such as those built for gaming.
  • Direct Binary Interface to OpenMM: The library provides a direct binary interface that allows seamless integration with ICM molecular objects. This integration facilitates the passing of these molecular objects to the MD engine and enables the efficient collection of trajectory snapshots into the ICM conformational stack.
  • Harmonic Tethers and Distance Restraints: The library supports the use of harmonic tethers and distance restraints, which can be specified using the options tether and drestraint. These features allow for the application of constraints to maintain certain distances or angles during simulations.
  • Snapshot Storage: Trajectory snapshots are stored in the ICM (Internal Coordinate Mechanics) stack at regular time intervals. This feature enables the efficient tracking and analysis of molecular conformations over time.
  • Explicit Water Simulations: For simulations involving explicit water molecules, it is essential to ensure that all atom types, charges, and the water box are correctly defined and filled. This requirement is crucial for the accuracy and stability of the MD simulations.
  • Membrane Simulations and Embedding: The option 'membrane' activates specialized non-isotropic barostat in OpenMM (separate pressure along Z axis and tension in XY plane).

These features make OpenMM inside ICM-Pro a powerful tool for researchers looking to perform high-speed MD simulations on cost-effective hardware.

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.

To run an MD simulation in a Membrane.

  • Convert your protein to an ICM object.
  • MolMechanics/Run MD Simulation - Click on the Membrane tab.
  • Select a region of your protein around which you wish to center the membrane. It implements a basic membrane embedding using a pre-built lipid bilayer (~95x95Å POPE/POPC mix).
  • You can choose the option to perform embedding of the membrane before the simulation starts which will make sure all waters are all removed from the membrane before the main simulation begins.

Results:

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 - Select a pair of atoms or use green and orange selections for closest distance. A table and plots of the distance will be displayed.
  • 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
  • RMSF - Root mean square fluctuation indicates positional differences in structure during a simulation. There is a Static and Superimpose option - the superimpose option follows protocol described here. You can provide two selections: for superposition using orange selection and regular "green" selection for RMSF calculation. By default it (if no selections are provided) backbone from all residues will be used.
  • Ligand Contacts - This method uses our Interaction Lists macro from our docking hitlist. Select the ligand and then the macro will be called for each MD snapshot in the stack and calculates number of: hydrophobic(apol), hydrogen bond don/acc (hba/hbd) and positive/negative. Individual residues can be included if you check this opti
  • Torsion - Select a pair of atoms on a rotatable bond to calculate the torsion angle.
  • Area - 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.


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