# \#molecular-simulation

**URL:** https://discourse.julialang.org/tag/molecular-simulation/1811.md

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## [PDBTools.jl: A Lightweight and High-Performance Julia Package for Molecular Structure File Handling and Analysis](https://discourse.julialang.org/t/pdbtools-jl-a-lightweight-and-high-performance-julia-package-for-molecular-structure-file-handling-and-analysis/137191)

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**Author:** [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Replies:** 0\
**Last updated:** [May 19, 2026, 12:06pm UTC](https://discourse.julialang.org/t/pdbtools-jl-a-lightweight-and-high-performance-julia-package-for-molecular-structure-file-handling-and-analysis/137191 "2026-05-19T12:06:31Z")

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I’m glad to inform the publication of the article describing the current features of PDBTools.jl : PDBTools.jl: A Lightweight and High-Performance Julia Package for Molecular Structure File Handling and Analysis https:/…

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## [Solvent Accessible Surface Area](https://discourse.julialang.org/t/solvent-accessible-surface-area/132751)

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**Author:** [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Replies:** 2\
**Last updated:** [October 1, 2025, 9:36pm UTC](https://discourse.julialang.org/t/solvent-accessible-surface-area/132751 "2025-10-01T21:36:06Z")

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For anyone that might be interested, we implemented a molecular Solvent Accessible Surface Area calculator in PDBTools.jl: The interface is useful (for us) for allowing extracting contributions to the SASA very easily…

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## [\[ANN\] YetAnotherSimulationSuite.jl: An atomic simulation suite](https://discourse.julialang.org/t/ann-yetanothersimulationsuite-jl-an-atomic-simulation-suite/132398)

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**Author:** [@Cavenfish](https://discourse.julialang.org/u/Cavenfish)\
**Replies:** 2\
**Last updated:** [September 15, 2025, 2:56pm UTC](https://discourse.julialang.org/t/ann-yetanothersimulationsuite-jl-an-atomic-simulation-suite/132398 "2025-09-15T14:56:10Z")

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YetAnotherSimulationSuite.jl (YASS) aims to offer users a simple, intuitive and easy-to-use atomic simulation suite. It draws inspiration from Python’s ASE, but is intended to be faster and offer users more flexibility. …

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## [Issue with Atom Selection mddf calculation (ComplexMixtures.jl from python)](https://discourse.julialang.org/t/issue-with-atom-selection-mddf-calculation-complexmixtures-jl-from-python/129604)

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**Author:** [@SnehaSahuvs4](https://discourse.julialang.org/u/SnehaSahuvs4)\
**Replies:** 10\
**Last updated:** [June 9, 2025, 9:43am UTC](https://discourse.julialang.org/t/issue-with-atom-selection-mddf-calculation-complexmixtures-jl-from-python/129604 "2025-06-09T09:43:55Z")

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Hi @lmiq I’m encountering an issue when calculating the center of mass using cm.select(). Specifically, it seems that the selection is not correctly including all the specified residues. For example, whether I use: pr…