ArticleJournal of chemical theory and computation2022
Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes.The journal of physical chemistry. B · 2024Article
- Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks.Journal of chemical theory and computation · 2024Article
- Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin.Biophysical journal · 2023Article
- Molecular Modelling of Ionic Liquids: Situations When Charge Scaling Seems Insufficient.Molecules (Basel, Switzerland) · 2023Article
- Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.Biophysical reviews · 2022Review
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4 authors.
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Abstract
Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala
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