Literature DB >> 26588507

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation.

James F Dama1, Grant Rotskoff1, Michele Parrinello2,3, Gregory A Voth1.   

Abstract

Well-tempered metadynamics has proven to be a practical and efficient adaptive enhanced sampling method for the computational study of biomolecular and materials systems. However, choosing its tunable parameter can be challenging and requires balancing a trade-off between fast escape from local metastable states and fast convergence of an overall free energy estimate. In this article, we present a new smoothly convergent variant of metadynamics, transition-tempered metadynamics, that removes that trade-off and is more robust to changes in its own single tunable parameter, resulting in substantial speed and accuracy improvements. The new method is specifically designed to study state-to-state transitions in which the states of greatest interest are known ahead of time, but transition mechanisms are not. The design is guided by a picture of adaptive enhanced sampling as a means to increase dynamical connectivity of a model's state space until percolation between all points of interest is reached, and it uses the degree of dynamical percolation to automatically tune the convergence rate. We apply the new method to Brownian dynamics on 48 random 1D surfaces, blocked alanine dipeptide in vacuo, and aqueous myoglobin, finding that transition-tempered metadynamics substantially and reproducibly improves upon well-tempered metadynamics in terms of first barrier crossing rate, convergence rate, and robustness to the choice of tuning parameter. Moreover, the trade-off between first barrier crossing rate and convergence rate is eliminated: the new method drives escape from an initial metastable state as fast as metadynamics without tempering, regardless of tuning.

Entities:  

Year:  2014        PMID: 26588507     DOI: 10.1021/ct500441q

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  14 in total

1.  Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations.

Authors:  Fikret Aydin; Rui Sun; Jessica M J Swanson
Journal:  Biophys J       Date:  2019-05-21       Impact factor: 4.033

Review 2.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

3.  Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.

Authors:  Rui Sun; Yining Han; Jessica M J Swanson; Jeffrey S Tan; John P Rose; Gregory A Voth
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

4.  Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling.

Authors:  Michele Invernizzi; Michele Parrinello
Journal:  J Chem Theory Comput       Date:  2022-05-26       Impact factor: 6.578

5.  Determinants of Endoplasmic Reticulum-to-Lipid Droplet Protein Targeting.

Authors:  Maria-Jesus Olarte; Siyoung Kim; Morris E Sharp; Jessica M J Swanson; Robert V Farese; Tobias C Walther
Journal:  Dev Cell       Date:  2020-07-29       Impact factor: 12.270

6.  Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

Authors:  Ian J Nessler; Jacob M Litman; Michael J Schnieders
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

Review 7.  Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

Authors:  D Wu; M I Fajer; L Cao; X Cheng; W Yang
Journal:  Methods Enzymol       Date:  2016-06-23       Impact factor: 1.600

8.  Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

Authors:  Siyoung Kim; Gregory A Voth
Journal:  J Phys Chem B       Date:  2021-06-17       Impact factor: 2.991

9.  Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.

Authors:  Chenghan Li; Jessica M J Swanson
Journal:  J Phys Chem B       Date:  2020-06-24       Impact factor: 2.991

10.  Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction.

Authors:  James F Dama; Glen M Hocky; Rui Sun; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2015-11-20       Impact factor: 6.006

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