Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2024 Jan 4;15:240. doi: 10.1038/s41467-023-44528-w

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 5 — a Ball-and-stick representation of the unfolded and folded states of chignolin in explicit water solvent (5889 atoms), including a cartoon representation of the backbone in crimson. The white, gray, blue, and red spheres represent hydrogen, carbon, nitrogen, and oxygen atoms, respectively. b Two-dimensional free-energy surface of chignolin (see the “Methods” section for details), along a collective variable (CV) based on harmonic linear discriminant analysis (HLDA), and the C-alpha root-mean-square deviation (RMSD) from a folded configuration. The white star marks the initial configuration and the dashed line indicates the first-passage criterion. The white regions have free energy > 20 k_BT. c Speedup as a function of bias deposition rate for Metadynamics (MetaD) simulations using the HLDA-based CV, without stochastic resetting (SR) (green) and with optimal (opt.) SR (orange). d Speedup as a function of bias deposition rate for MetaD simulations using the RMSD as CV, with and without SR. Error bars represent standard deviation divided by the square-root of the number of independent trajectories (n = 1000). Source data are provided as a Source Data file.