{"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/ensuring-thermodynamic-consistency-with","title":"Ensuring thermodynamic consistency with invertible coarse-graining","arxiv_id":"2210.07882","date":"2022-10-14","proceeding":null,"authors":["Shriram Chennakesavalu","David J. Toomer","Grant M. Rotskoff"],"abstract":"Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared to atomistic models. Designing ``good'' coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We show that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.","url_abs":"https://arxiv.org/abs/2210.07882v1","url_pdf":"https://arxiv.org/pdf/2210.07882v1.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":"ensuring-thermodynamic-consistency-with","repo_url":"https://github.com/rotskoff-group/thermodynamic-consistency","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2210.07882","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}