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Analyzing and Biasing Simulations with PLUMED

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Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2022))

Abstract

This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free energy can be computed as a function of one or more collective variables. A number of practical issues mostly around periodic boundary conditions that arise when these types of calculations are performed using PLUMED are then discussed. Later parts of the chapter discuss how PLUMED can be used to perform enhanced sampling simulations that introduce simulation biases or multiple replicas of the system and Monte Carlo exchanges between these replicas. This section is then followed by a discussion on how free-energy surfaces and associated error bars can be extracted from such simulations by using weighted histogram and block averaging techniques.

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Acknowledgements

Writing and maintaining PLUMED involves a considerable amount of effort and we thus would like to finish by acknowledging everyone who has contributed to PLUMED in some way over the years. PLUMED 2 was developed by a team of five core developers that include the authors, Massimiliano Bonomi, Davide Branduardi, and Carlo Camilloni. Furthermore, Haochuan Chen, Haohao Fu, Glen Hocky, Omar Valsson, and Andrew White have all contributed modules to the code, whereas several other users have contributed other minor functionalities or fixed bugs in the code. Lastly, we would like to acknowledge the many users and developers who have emailed our user and developer lists or attended the various PLUMED tutorials and user meetings. The contributions of these people have been invaluable in terms of alerting us to bugs in the code.

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Authors and Affiliations

  1. Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy

    Giovanni Bussi

  2. Atomistic Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast, UK

    Gareth A. Tribello

Authors
  1. Giovanni Bussi
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  2. Gareth A. Tribello
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Corresponding authors

Correspondence to Giovanni Bussi or Gareth A. Tribello .

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Editors and Affiliations

  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Bussi, G., Tribello, G.A. (2019). Analyzing and Biasing Simulations with PLUMED. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_21

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  • DOI: https://doi.org/10.1007/978-1-4939-9608-7_21

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