Literature DB >> 29733652

Collective Variables from Local Fluctuations.

Dan Mendels1,2, GiovanniMaria Piccini1,2, Michele Parrinello1,2.   

Abstract

We introduce a method to obtain one-dimensional collective variables for studying rarely occurring transitions between two metastable states separated by a high free energy barrier. No previous information, not even approximated, on the path followed during the transition is needed. The only requirement is to know the fluctuations of the system while in the two metastable states. With this information in hand, we build the collective variable using a modified version of Fisher's linear discriminant analysis. The usefulness of this approach is tested on the metadynamics simulation of two representative systems. The first is the freezing of silver iodide into the superionic α-phase, and the second is the study of a classical Diels-Alder reaction. The collective variable works very well in these two diverse cases.

Entities:  

Year:  2018        PMID: 29733652     DOI: 10.1021/acs.jpclett.8b00733

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  12 in total

1.  Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

Authors:  Peng He; Bin W Zhang; Shima Arasteh; Lingle Wang; Robert Abel; Ronald M Levy
Journal:  J Phys Chem Lett       Date:  2018-07-24       Impact factor: 6.475

2.  Deep learning the slow modes for rare events sampling.

Authors:  Luigi Bonati; GiovanniMaria Piccini; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-02       Impact factor: 11.205

3.  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

4.  SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.

Authors:  Zhe Huai; Huaiyu Yang; Xiao Li; Zhaoxi Sun
Journal:  J Comput Aided Mol Des       Date:  2020-10-10       Impact factor: 3.686

5.  Data-driven reaction coordinate discovery in overdamped and non-conservative systems: application to optical matter structural isomerization.

Authors:  Shiqi Chen; Curtis W Peterson; John A Parker; Stuart A Rice; Andrew L Ferguson; Norbert F Scherer
Journal:  Nat Commun       Date:  2021-05-05       Impact factor: 14.919

6.  The role of water in host-guest interaction.

Authors:  Valerio Rizzi; Luigi Bonati; Narjes Ansari; Michele Parrinello
Journal:  Nat Commun       Date:  2021-01-04       Impact factor: 14.919

7.  Free Energy Surfaces and Barriers for Vacancy Diffusion on Al(100), Al(110), Al(111) Reconstructed Surfaces.

Authors:  Junais Habeeb Mokkath; Mufasila Mumthaz Muhammed; Ali J Chamkha
Journal:  Nanomaterials (Basel)       Date:  2021-12-28       Impact factor: 5.076

Review 8.  Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments.

Authors:  Soumendranath Bhakat
Journal:  RSC Adv       Date:  2021-03-17       Impact factor: 3.361

9.  Molecular Insights from Conformational Ensembles via Machine Learning.

Authors:  Oliver Fleetwood; Marina A Kasimova; Annie M Westerlund; Lucie Delemotte
Journal:  Biophys J       Date:  2019-12-21       Impact factor: 4.033

Review 10.  Collective variable-based enhanced sampling and machine learning.

Authors:  Ming Chen
Journal:  Eur Phys J B       Date:  2021-10-20       Impact factor: 1.500

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