The calculation of the potential of mean force using computer simulations

Scalable molecular dynamics with NAMD

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914

Dynamic personalities of proteins

Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Laio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619

Calculation of absolute protein–ligand binding free energy from computer simulations

Woo, H.-J., & Roux, B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409005102 · Cited by 661

Assessing the Accuracy of Metadynamics

Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045424k · Cited by 517

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008099 · Cited by 343

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Das, P., Moll, M., Stamati, H., Kavraki, L. E., & Clementi, C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603553103 · Cited by 331

PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling

Yen, H.-Y., Hoi, K. K., Liko, I., Hedger, G., Horrell, M. R., Song, W., Wu, D., Heine, P., Warne, T., Lee, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0325-6 · Cited by 284

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cournia, Z., Allen, T. W., Andricioaei, I., Antonny, B., Baum, D., Brannigan, G., Buchete, N.-V., Deckman, J. T., Delemotte, L., del Val, C., et al. (2015) · The Journal of Membrane Biology · doi:10.1007/s00232-015-9802-0 · Cited by 235

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

Abrams, J. B., & Tuckerman, M. E. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp805039u · Cited by 221

Automatic coarse graining of polymers

Faller, R. (2004) · Polymer · doi:10.1016/j.polymer.2003.11.053 · Cited by 115

Aspartic acid as a crystal growth catalyst

Piana, S., Jones, F., & Gale, J. D. (2007) · CrystEngComm · doi:10.1039/b708260f · Cited by 68

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

Periole, X. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00344 · Cited by 58

Structural insights into the effects of 2’-5’ linkages on the RNA duplex

Sheng, J., Li, L., Engelhart, A. E., Gan, J., Wang, J., & Szostak, J. W. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317799111 · Cited by 50

Computational DNA binding studies of (–)-epigallocatechin-3-gallate

Galindo-Murillo, R., & Cheatham, T. E. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1389306 · Cited by 27

Gated CO2 permeation across dynamic graphene pores

Bondaz, L., Ronghe, A., Ganapathy Ayappa, K., & Agrawal, K. V. (2025) · Nature Communications · doi:10.1038/s41467-025-61518-2 · Cited by 12

OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking

Borgmans, S., Rogge, S. M. J., Vanduyfhuys, L., & Van Speybroeck, V. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01028 · Cited by 8

Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations

Giorgino, T., Harvey, M. J., & de Fabritiis, G. (2010) · Computer Physics Communications · doi:10.1016/j.cpc.2010.04.007 · Cited by 8

Computational design of Bax-inhibiting peptides

Vlaar, T., Mayer, B., van der Heide, L., & Ilie, I. M. (2025) · Materials Advances · doi:10.1039/d4ma01142b · Cited by 2

The repetitive local sampling and the local distribution theory

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