upward

Molecular metadynamics and kinetics

Potential energy landscape

D J Wales, Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape, JCP 142, 130901 (2015)

Statistical sampling

Parallel tempering (Wikipedia)


M Invernizzi, P M Piaggi, M Parrinello, Unified Approach to Enhanced Sampling, PRX 10, 041034 (2020)

Y Sugita, Y Okamoto, Replica-exchange molecular dynamics method for protein folding, CPL 314, 141 (1999)

Transition path

Transition path sampling (Wikipedia)

Transition path sampling, ed Bolhuis P (2004)


P Bolhuis, D Swenson, Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook, ATS 4, 2000237 (2021) – doi

W E, E Vanden-Eijnden, Transition-path theory and path-finding algorithms for the study of rare events, ARPC 61, 391 (2010)


S Beccara, G Garberoglio, P Faccioli, F Pederiva, Ab initio dynamics of rare thermally activated reactions, JCP 132, 111102 (2010)

Pan A C, Roux B, Building Markov state models along pathways to determine free energies and rates of transitions, JCP 129, 064107 (2008)

Pan A C, Sezer D, Roux B, Finding transition pathways using the string method with swarms of trajectories, JPCB 112, 3432 (2008)

Maragliano L, Fischer A, Vanden-Eijnden E, Ciccotti G, String method in collective variables: Minimum free energy paths and isocommittor surfaces, JCP 125, 024106 (2006)

Metadynamics

A Laio, F L Gervasio, Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science, RPP 71, 126601 (2008)

A F Voter, F Montalenti, T C Germann, Extending the Time Scale in Atomistic Simulation of Materials, ARMR 32, 321 (2002)


U Sengupta, M Carballo-Pacheco, B Strodel, Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly, JCP 150, 115101 (2019)

G Henkelman, H Jonsson, Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table, JCP 115, 9657 (2001)

M R Sorensen, A F Voter, Temperature-accelerated dynamics for simulation of infrequent events, JCP 112, 9599 (2000)

Kinetics

J Daldrop, J Kappler, F Brunig, R Netz, Butane dihedral angle dynamics in water is dominated by internal friction, PNAS 115, 5169 (2018)

J H Prinz, H Wu, M Sarich, B Keller, M Senne, M Held, J D Chodera, C Schutte, F Noe, Markov models of molecular kinetics: Generation and validation, JCP 134, 174105 (2011)