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Linking Well-Tempered Metadynamics Simulations with Experiments

Alessandro Barducci, Massimiliano Bonomi, Michele Parrinello
2010 Biophysical Journal  
Even if such bias distorts the probability distribution of the other degrees of freedom, the equilibrium Boltzmann distribution can be reconstructed using a recently developed reweighting algorithm.  ...  Here we show the potential of this combined approach by characterizing the conformational ensemble explored by a 13-residue helix-forming peptide by means of a well-tempered metadynamics/parallel tempering  ...  ACKNOWLEDGMENTS The authors thank ''Centro Enrico Fermi'' for providing the computational resources.  ... 
doi:10.1016/j.bpj.2010.01.033 pmid:20441734 pmcid:PMC2862196 fatcat:rhhja4uqlbhitkp73guuw67xta

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

Cameron Abrams, Giovanni Bussi
2013 Entropy  
We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods.  ...  In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration  ...  Conflicts of Interest The authors declare no conflict of interest.  ... 
doi:10.3390/e16010163 fatcat:iqdr2qne3vcfjaovn3tjvcdlpi

Enhanced sampling methods for molecular dynamics simulations [article]

Jérôme Hénin, Tony Lelièvre, Michael R. Shirts, Omar Valsson, Lucie Delemotte
2022 arXiv   pre-print
We then illustrate in which ways many different methods combine principles from a smaller class of enhanced sampling concepts.  ...  To enable comparisons, the various methods are introduced using the same terminology and notation.  ...  Well-Tempered Ensemble The well-tempered ensemble [132] is obtained by using the potential energy U as CV within well-tempered metadynamics.  ... 
arXiv:2202.04164v1 fatcat:rhb7bd4xo5b4hewmroy6eqhmna

Iterative unbiasing of quasi-equilibrium sampling [article]

Federico Giberti, Bingqing Cheng, Gareth Aneurin Tribello, Michele Ceriotti
2019 arXiv   pre-print
Efficient re-weighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as Metadynamics, Variationally Enhanced Sampling or Parallel Bias Metadynamics  ...  , in which the system evolves in a quasi-equilibrium manner under a time-dependent bias.  ...  BC acknowledges funding from SNSF (Project P2ELP2-184408).  ... 
arXiv:1911.01140v2 fatcat:krfohin2lvgildinzpmfzbdvli

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics

François Sicard, Patrick Senet
2013 Journal of Chemical Physics  
Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins.  ...  WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics.  ...  Conclusion and Discussion In this paper, we considered a Well-Tempered metadynamics approach coupled with biased collective variables generated from a dihedral principal component analysis to reconstruct  ... 
doi:10.1063/1.4810884 pmid:23802984 fatcat:qsd73zivsbgh3dwqxfnbywomoe

Time-independent free energies from metadynamics via Mean Force Integration [article]

Veselina Marinova, Matteo Salvalaglio
2019 arXiv   pre-print
Moreover, MFI naturally extends to aggregate information obtained from independent metadynamics simulations, allowing to converge free energy surfaces without the need to sample recrossing events in a  ...  MFI circumvents the need for computing the ensemble average of the bias acting on the system c(t) and can be applied to different variants of metadynamics.  ...  We acknowledge the Legion High Performance Computing Facility for access to Legion@UCL and associated support services in the completion of this work.  ... 
arXiv:1907.08472v4 fatcat:a2b3oxkrkrdehjsnoesz2nn7pq

From Metadynamics to Dynamics

Pratyush Tiwary, Michele Parrinello
2013 Physical Review Letters  
needed over ordinary metadynamics.  ...  Metadynamics is a commonly used and successful enhanced sampling method.  ...  The authors thank David Chandler for theoretical insight, and Ali Hassanali and Matteo Salvalaglio for useful and stimulating discussions.This work was funded by the European Union (Grant ERC-2009-AdG-  ... 
doi:10.1103/physrevlett.111.230602 pmid:24476246 fatcat:khorn4ck35gbbi66dt5wehbvle

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

Simone Marsili, Giorgio Federico Signorini, Riccardo Chelli, Massimo Marchi, Piero Procacci
2009 Journal of Computational Chemistry  
The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular  ...  ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at  ...  Finally, following the well-tempered metadynamics approach, 39 the third choice is given by F(z) = −V P z,t (add) = e −V (z,t)/kBT , (23) where the probability depends both on time t and on position z  ... 
doi:10.1002/jcc.21388 pmid:19824035 fatcat:q5d4elndwbhnracq4q4evug634

Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead

Fabio Pietrucci
2017 Reviews in Physics  
This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems.  ...  The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines.  ...  This argument is pertinent to the original metadynamics formulation, with fixed Gaussian height W 0 : in an alternative formulation, well-tempered metadynamics 73 , the height is progressively reduced  ... 
doi:10.1016/j.revip.2017.05.001 fatcat:igpkfs6h7rg4ndmjzur4lefeq4

Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics [article]

C. Camilloni, D. Provasi, G. Tiana, R. A. Broglia
2007 arXiv   pre-print
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm.  ...  Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling with an affordable computational effort.  ...  Since each replica experiences a different potential due to the bias from the non-Markovian metadynamics terms, as well as to the scaling from the solute tempering scheme, the acceptance probability must  ... 
arXiv:0707.1230v1 fatcat:smalvghgo5azvfgndikayze36q

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

Marco A. Deriu, Gianvito Grasso, Jack A. Tuszynski, Diego Gallo, Umberto Morbiducci, Andrea Danani, James M. Briggs
2016 PLoS Computational Biology  
Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states.  ...  We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation.  ...  Metadynamics The first eigenvector derived from the PCA was used as collective variable (CV) for a well-tempered Metadynamics simulation.  ... 
doi:10.1371/journal.pcbi.1004699 pmid:26745628 pmcid:PMC4706304 fatcat:xrzmtk4mybfkhoykvsrqf6pilm

Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

Carlo Camilloni, Fabio Pietrucci
2018 Advances in Physics: X  
The main focus is on established techniques and emerging trends in the fields of enhanced sampling and of kinetic models, as applied to biological problems ranging from protein folding and conformational  ...  We address especially the following questions: How to choose a computational approach suited to a particular problem? What are the strengths and limitations of alternative approaches?  ...  Disclosure statement No potential conflict of interest was reported by the authors.  ... 
doi:10.1080/23746149.2018.1477531 fatcat:ons7cobxerg4bgxpgjndbtvkl4

Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR

Carlo Camilloni, Daniel Schaal, Kristian Schweimer, Stephan Schwarzinger, Alfonso De Simone
2012 Biophysical Journal  
We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides.  ...  In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a  ...  Michele Parrinello (Swiss Federal Institute of Technology Zurich) for discussions and critical reading of the manuscript.  ... 
doi:10.1016/j.bpj.2011.12.003 pmid:22225810 pmcid:PMC3250675 fatcat:hluaovebhva6nfpjipfktdvvca

DNA Base Pair Mismatches Induce Structural Changes and Alter the Free Energy Landscape of Base Flip [article]

Addie Kingsland, Lutz Maibaum
2018 arXiv   pre-print
We utilize molecular dynamics and metadynamics computer simulations to study the equilibrium structure and dynamics for both matched and mismatched base pairs.  ...  Mismatched pairs shift further in the plane normal to the DNA strand and are more likely to exhibit non-canonical structures, including the e-motif.  ...  Acknowledgments The authors wish to thank Jim Pfaendtner and Patrick Burney for advice on metadynamics simulations.  ... 
arXiv:1803.02027v1 fatcat:yhtj7adrrjet5grpkar4vfo4b4

Mean Force Based Temperature Accelerated Sliced Sampling: Efficient Reconstruction of High Dimensional Free Energy Landscapes [article]

Asit Pal, Subhendu Pal, Shivani Verma, Motoyuki Shiga, Nisanth N. Nair
2021 arXiv   pre-print
umbrella sampling and metadynamics.  ...  The WHAM necessitates that TASS windows lie close to each other for proper overlap of distributions and span the collective variable space of interest.  ...  It is preferred to choose V b (z, t) = τ <t w τ exp − {z − z τ } 2 2(δz) 2 (5) with w τ = ω 0 exp − V b (z τ , τ ) k B ∆T , (6) and z τ ≡ z(τ ) as in well-tempered metadynamics (WT-MTD). 37, 38 In the  ... 
arXiv:2106.03321v1 fatcat:o2kuoxujpbaldm2lo3mk224upm
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