{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/performing-all-atom-molecular-dynamics","title":"Performing all-atom molecular dynamics simulations of intrinsically disordered proteins with replica exchange solute tempering","arxiv_id":"2505.01860","date":"2025-05-03","proceeding":null,"authors":["Jaya Krishna Koneru","Korey M. Reid","Paul Robustelli"],"abstract":"All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain structures with many distinct topologies separated by large free-energy barriers. Sampling the vast conformational space of IDPs in explicit solvent all-atom MD simulations is extremely challenging, and enhanced sampling methods are generally required to obtain statistically meaningful descriptions of IDP conformational ensembles. Replica exchange solute tempering (REST) methods, where multiple coupled simulations of a system are performed in parallel with selectively modified potential energy functions, are a powerful approach for efficiently sampling the conformational space of IDPs. In this chapter, we demonstrate how to set-up, perform and analyze all-atom MD simulations of IDPs with REST enhanced sampling methods.","url_abs":"https://arxiv.org/abs/2505.01860v1","url_pdf":"https://arxiv.org/pdf/2505.01860v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"performing-all-atom-molecular-dynamics","repo_url":"https://github.com/paulrobustelli/idp_rest_tutorial","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}