ArticleThe journal of physical chemistry. B2024
Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of A
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Bio-Inspired Peptide Membranes for COThe journal of physical chemistry. B · 2026Article
- Temperature Effects on the Structural Stability of EFACS materials Au · 2026Article
- Mechanistic In-Silico Insights into the Anti-quorum Sensing Potential of Coumaric Acid and Syringic Acid in Serratia marcescens with Invitro Analysis.The protein journal · 2025Article
- Molecular Dynamics Simulations of Self-Assembled EACS physical chemistry Au · 2025Article
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2 authors.
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Abstract
This work presents a study on the effects of periodic boundary conditions (PBC) on the energetic/structural properties and hydrogen bond dynamics (HB) using molecular dynamics (MD) simulations of peptide membranes composed of alanine and histidine. Our results highlight that simulations using small surface areas for the peptide membrane may result in nonconvergent values for membrane properties, which are only observed in regions simulated at a certain distance from the PBCs. Specifically, regarding hydrogen bonds, a property pervasive in peptide membranes, our findings indicate a significant increase in the lifetime of these interactions, reaching values ∼19% higher when observed in structures free from PBCs. For peptide mobility in these nanomembranes, our results compare regions simulated directly under the influence of PBCs with regions free from these conditions, emphasizing greater mobility of amino acid psi/phi angles in the latter model.
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