Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM-Reference-Cited by-同舟云学术

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Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM

Published:2024-04-25 Issue:9 Volume:20 Page:3492-3502
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Sasmal Subarna¹^ORCID,Pal Triasha¹,Hocky Glen M.¹²^ORCID,McCullagh Martin³^ORCID

Affiliation:

1. Department of Chemistry, New York University, New York, New York 10003, United States

2. Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, United States

3. Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States

Funder

Division of Chemistry

National Institute of Allergy and Infectious Diseases

New York University

National Institute of General Medical Sciences

Publisher

American Chemical Society (ACS)

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.4c00223

Reference59 articles.

1. Escaping free-energy minima

2. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

3. Calculating free energies using average force

4. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

5. A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations

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