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FRESEAN-metadynamics

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@HeydenLabASU HeydenLabASU released this 17 Jun 00:33
· 34 commits to main since this release
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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
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