References

[1] Romelia salomon ferrer, David Case, and Ross Walker. An overview of the amber biomolecular simulation package. Wiley Interdisciplinary Reviews: Computational Molecular Science, 3, 03 2013.

[2] Henk Bekker, Herman Berendsen, E.J. Dijkstra, S. Achterop, Rudi Drunen, David van der Spoel, A. Sijbers, H. Keegstra, B. Reitsma, and M.K.R. Renardus. Gromacs: A parallel computer for molecular dynamics simulations. Physics Computing, 92:252–256, 01 1993.

[3] Peter Eastman, Jason Swails, John Chodera, Robert Mcgibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew Simmonett, Matthew Harrigan, Chaya Stern, Rafal Wiewiora, Bernard Brooks, and Vijay Pande. Openmm 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol, 06 2017.

[4] Aidan Thompson, H. Metin Aktulga, Richard Berger, Dan Bolintineanu, W. Brown, Paul Crozier, Pieter in ’t Veld, Axel Kohlmeyer, Stan Moore, Trung Nguyen, Ray Shan, Mark Stevens, J. Tranchida, Christian Trott, and Steven Plimpton. Lammps - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics communications, 271:108171, 09 2021.

[5] Zhou Ruhong. Replica exchange molecular dynamics method for protein folding simulation. Methods in molecular biology (Clifton, N.J.), 350:205–23, 02 2007.

[6] Lijiang Yang and Yi Gao. A selective integrated tempering method. The Journal of chemical physics, 131:214109, 12 2009.

[7] Alessandro Barducci and Massimiliano Bonomi. Metadynamics. WIREs Comput. Mol. Sci., 1:826, 09 2011.

[8] Luigi Bonati, Yue-Yu Zhang, and Michele Parrinello. Neural networks-based variationally enhanced sampling. Proceedings of the National Academy of Sciences, 116:201907975, 08 2019.

[9] Dongdong Wang, Yanze Wang, Junhan Chang, Linfeng Zhang, Han Wang, et al. Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics. Nature Computational Science, 2(1):20–29, 2022.

[10] Linfeng Zhang, Jiequn Han, Han Wang, Roberto Car, and Weinan E. Deep potential molecular dynamics: a scalable model with the accuracy of quantum mechanics. July 2017.

[11] Luigi Bonati, Valerio Rizzi, and Michele Parrinello. Data-driven collective variables for enhanced sampling. The Journal of Physical Chemistry Letters, 11:2998–3004, 04 2020.