This extension allows you to setup and run simulations with the OpenMM package.

It will automatically install the required OpenMM Python packages in your SAMSON, including packages to run on Nvidia GPUs using CUDA and AMD GPUs using HIP6. You can choose the platform in the advanced parameters.

Documentation

1. Choose the input system - it can be PDB/mmCIF (prepared with, for example, PDBFixer), Amber, or CHARMM.
2. Setup simulation by modifying OpenMM parameters.
3. Run simulation. The OpenMM Wizard will generate a Python script to run OpenMM. You can also run the simulation elsewhere by utilizing the Python script generated for you.

Related extensions

• PDBFixer
• GROMACS Wizard

References

P. Eastman, R. Galvelis, R. P. Peláez, C. R. A. Abreu, S. E. Farr, E. Gallicchio, A. Gorenko, M. M. Henry, F. Hu, J. Huang, A. Krämer, J. Michel, J. A. Mitchell, V. S. Pande, J. PGLM Rodrigues, J. Rodriguez-Guerra, A. C. Simmonett, S. Singh, J. Swails, P. Turner, Y. Wang, I. Zhang, J. D. Chodera, G. De Fabritiis, and T. E. Markland. “OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.” J. Phys. Chem. B 128(1), pp. 109-116 (2023) https://doi.org/10.1021/acs.jpcb.3c06662