Literature DB >> 17302470

From A to B in free energy space.

Davide Branduardi1, Francesco Luigi Gervasio, Michele Parrinello.   

Abstract

The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.

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Year:  2007        PMID: 17302470     DOI: 10.1063/1.2432340

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  99 in total

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Review 8.  Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Authors:  Paraskevi Gkeka; Gabriel Stoltz; Amir Barati Farimani; Zineb Belkacemi; Michele Ceriotti; John D Chodera; Aaron R Dinner; Andrew L Ferguson; Jean-Bernard Maillet; Hervé Minoux; Christine Peter; Fabio Pietrucci; Ana Silveira; Alexandre Tkatchenko; Zofia Trstanova; Rafal Wiewiora; Tony Lelièvre
Journal:  J Chem Theory Comput       Date:  2020-07-16       Impact factor: 6.006

9.  Finding transition pathways using the string method with swarms of trajectories.

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Journal:  J Phys Chem B       Date:  2008-02-22       Impact factor: 2.991

10.  Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations.

Authors:  Dalibor Trapl; Izabela Horvacanin; Vaclav Mareska; Furkan Ozcelik; Gozde Unal; Vojtech Spiwok
Journal:  Front Mol Biosci       Date:  2019-04-18
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