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.

On the command line use runMDopenMM.icm script which is located in the $ICMHOME/bin directory.

Syntax:

 icm runMDopenMM.icm input.ob options

Options:

• -ng : don't use GPU even if detected
• -w : add water
• time= : simulation length in nanoseconds
• confs= : number of snapshots to store in the stack
• rep= : run multiple (number of repeats) trajectories from the provided starting point
• -m : apply icm minimization/relaxation before the MD run
• -rl : restrain parts of the system far from ligand (default is heteroatom molecule, lig= can be used to select ligand as desired)
• -tl : like -rl but tether to initial positions instead of internal distance restraints
• -E : embed into a pre-built POPC/POPE lipid membrane and run in membrane mode
• center= : in conjunction with -E, center membrane on selected residue
• -M : membrane mode, assuming pre-embedded input. Box must be consistent with periodic membrane
• -B : print A LOT of debug info
• BOX= : define box by two corners (min/max xyz). A custom box can be used but in MD the box must cover the entire object, with some margin. Box is used to create periodic system, where everything repeats in adjacent boxes. In general, there is rarely a good reason to not use automatic default. If one does use custom box, it is to make it bigger, not smaller.
• output= : name of the output object with an embedded stack of snapshots
• ligfile= : run a series of MD simulations, combining each ligand from filename.icb or filename.sdf with target protein
• gpuid= : GPU device index to run simulation on. Default 0