PLUMED Plugin Integration into High Performance Pmemd Program for Enhanced Molecular Dynamics Simulations
Keywords:High performance pmemd program, enhanced molecular dynamics simulations, PLUMED plugin integration, metadynamics, CUDA, GPU
Metadynamics as an enhanced sampling procedure of molecular dynamics simulations is an effective tool to simulate complex molecular motions, conformations and reactivity, including enzyme plasticity and catalysis. The classic non-enhanced molecular simulation tools have reached unprecedently high performance utilizing GPU units, however their implementation for enhanced sampling are still on demand. The widespread AMBER (molecular dynamics package) + PLUMED (metadynamics plugin) still does not take advantage of GPU computing or the CPU utilization optimization included in the AMBER pmemd program. In this work we have developed PLUMED binding to pmemd program resolving performance issues within hybrid molecular dynamics/metadynamics runs. Preliminary checks and test results of the model system have validated this implementation.
Case, D.A., Aktulga, H.M., Belfon, K., et al.: Amber 2021. University of California Press (2021), http://ambermd.org/doc12/Amber21.pdf
Laio, A., Parrinello, M.: Escaping free-energy minima. Proceedings of the National Academy of Sciences 99(20), 12562–12566 (2002). https://doi.org/10.1073/pnas.202427399
Qi, R., Wei, G., Ma, B., Nussinov, R.: Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example, pp. 101–119. Springer, New York, NY (2018). https://doi.org/10.1007/978-1-4939-7811-3_5
The PLUMED Consortium: Plumed 2 source code repository. Pull request #486 (2019), https://github.com/plumed/plumed2/pull/486
The PLUMED Consortium: Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods 16(8), 670–673 (2019). https://doi.org/10.1038/s41592-019-0506-8
The PLUMED Consortium: The PLUMED manual, version 2.7 (2020), https://www.plumed.org/doc-v2.7/developer-doc/html/_how_to_plumed_your_m_d.html
Voevodin, V.V., Antonov, A.S., Nikitenko, D.A., et al.: Supercomputer Lomonosov-2: Large scale, deep monitoring and fine analytics for the user community. Supercomputing Frontiers and Innovations 6(2), 4–11 (2019). https://doi.org/10.14529/jsfi190201
How to Cite
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-Non Commercial 3.0 License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.