GPU-Accelerated Molecular Dynamics with ICM-Pro - Common Questions

[Andrew Orry]

With built-in OpenMM support, MolSoft ICM-Pro brings fast, GPU-accelerated molecular dynamics simulations into a seamless and user-friendly interface. Below is a summary of the MD capabilities and workflows available in ICM-Pro, from system setup to advanced trajectory analysis. 

You can run MD in the ICM-Pro GUI using MolMechanics/Molecular Dynamics or on the command line in batch using the script runMDopenMM.icm in the /bin directory of your ICM distribution.

Q: What MD engine does MolSoft ICM-Pro use for molecular dynamics simulations?

A: ICM-Pro includes built-in support for OpenMM, a GPU-accelerated molecular dynamics engine (Eastman et al., 2017), providing a fast and efficient simulation environment.

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Q: How fast are MD simulations in ICM-Pro with GPU acceleration?

A: On a standard workstation GPU (such as those in gamer-class machines), ICM-Pro achieves speeds of approximately 3–12 ps/s, or 0.2–1.0 μs/day.

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Q: How is OpenMM integrated into ICM-Pro?

A: ICM-Pro provides a direct binary interface to OpenMM, allowing:

• Seamless transfer of molecular objects to the MD engine

• Automatic collection of trajectory snapshots into the ICM conformational stack for downstream analysis and visualization

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Q: How does ICM-Pro help prepare a system for MD simulations?

A: ICM-Pro offers a scriptable and GUI-based workflow for automated system preparation, including:

• Solvation in a periodic water box

• Assignment of AMBER atom types and charges

• Generation of AM1-BCC charges for ligands

• Initial energy minimization

• Application of tethers or distance restraints

• Use of the AMBER ff14SB force field for proteins

• Support for membrane systems

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Q: What tools are available in ICM-Pro for analyzing MD trajectories?

A: Users can compute and visualize a wide range of structural and energetic metrics, including:

• Interatomic distances

• RMSD and RMSF

• Contact areas and interaction types

• Side-chain torsions (e.g., chi1 angles)

• RTCNN score drift over time

• GB/SA binding free energy (ΔG_bind)

• Radius of gyration

• Physics-based scoring functions

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Q: Does ICM-Pro support batch MD simulations for hitlist validation?

A: Yes. ICM-Pro supports batch MD simulations to validate virtual screening hits by:

• Using the runMDopenMM.icm script

• Running MD relaxation on each docked complex

• Collecting multiple conformers per complex

• Tracking RMSD and RTCNN score changes over time