Published June 17, 2025
| Version v1
Software
Open
FRESEAN-metadynamics with step-by-step instructions for HEWL
Description
This repository contains software developed for FREquency-SElective ANharmonic (FRESEAN) mode analysis of molecular vibrations in molecular dynamics trajectories. This can be combined with coarse-graining of all-atom trajectories (implemented for proteins) to minimize computational cost and memory requirements, while preserving information on the lowest frequency vibrations.
A tutorial includes all required input files to combine FRESEAN mode analysis with metadynamics simulations of hen egg white lysozyme to sample its conformational free energy landscape.
References:
- M. A. Sauer, M.Heyden, Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins, J. Chem. Theory Comput. 19, 5481-5490 (2023).
- S. Mondal, M. A. Sauer, M. Heyden, Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations, J. Phys. Chem. B 128, 7112-7120 (2024).
- M. A. Sauer, S. Mondal, B. Neff, S. Maiti, M. Heyden, Fast Sampling of Protein Conformational Dynamics, arXiv:2411.08154
Files
FRESEAN-metadynamics-0.1.zip
Files
(1.2 MB)
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Additional details
Funding
- U.S. National Science Foundation
- From Protein Structure Predictions to Dynamics 2154834
- National Institute of General Medical Sciences
- Understanding Essential Protein Dynamics through the Anharmonic Properties of Thermally Excited Vibrations R01GM148622
Software
- Repository URL
- https://github.com/HeydenLabASU-collab/FRESEAN-metadynamics
- Development Status
- Active