Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations.

ABSTRACT: We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on time scales faster than conformational transitions but describe a path of least resistance toward structural change. A key challenge is that harmonic approximations are ill-suited to characterize these vibrations, which are observed at far-infrared frequencies and are easily excited by thermal collisions at room temperature. Here, we approached this problem with a frequency-selective anharmonic (FRESEAN) mode analysis that does not rely on harmonic approximations and successfully isolates anharmonic low-frequency vibrations from short molecular dynamics

SUBMITTER: Mondal S 

PROVIDER: S-EPMC11584282 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature