tag:joss.theoj.org,2005:/papers/tagged/Molecular%20DynamicsJournal of Open Source Software2024-03-10T12:27:59ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/50672024-03-10T12:27:59Z2024-03-12T10:21:48ZProject RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugatesacceptedv1.0.12024-01-10 16:52:37 UTC952024-03-10 12:27:59 UTC920246293MoritzL.ObenauerDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0003-8140-9907KaiN.SpauszusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0006-0650-2273PolBeseniusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0000-0001-7478-4459FriederikeSchmidInstitute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128 Mainz, Germany0000-0002-5536-671810.21105/joss.06293https://doi.org/10.5281/zenodo.10776652Jupyter Notebook, Python, Bikeshedhttps://joss.theoj.org/papers/10.21105/joss.06293.pdfcheminformatics, molecular-dynamics-simulatiom, pdb-files, molecular-modelingtag:joss.theoj.org,2005:Paper/48582024-03-06T17:32:25Z2024-03-07T00:00:24Zcalorine: A Python package for constructing and sampling neuroevolution potential modelsacceptedv2.02023-10-21 15:02:27 UTC952024-03-06 17:32:25 UTC920246264EricLindgrenDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-8549-6839MagnusRahmDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-6777-0371ErikFranssonDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0001-5262-3339FredrikErikssonDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-7945-5483NicklasÖsterbackaDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-6043-4607ZheyongFanCollege of Physical Science and Technology, Bohai University, Jinzhou 121013, P. R. China0000-0002-2253-8210PaulErhartDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-2516-606110.21105/joss.06264https://doi.org/10.5281/zenodo.10723374Python, C++, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.06264.pdfcondensed matter, machine learning, interatomic potentials, force fields, molecular dynamics, neuroevolution, neural networktag:joss.theoj.org,2005:Paper/47052024-02-19T16:19:20Z2024-02-20T13:50:07Zkinisi: Bayesian analysis of mass transport from molecular dynamics simulationsaccepted0.7.02023-08-16 15:02:57 UTC942024-02-19 16:19:20 UTC920245984AndrewR.McCluskeyCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom, European Spallation Source ERIC, Ole Maaløes vej 3, 2200 København N, Denmark0000-0003-3381-5911AlexanderG.SquiresSchool of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0001-6967-3690JoshDunnCentre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom0000-0003-2659-0806SamuelW.ColesDepartment of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0001-9722-5676BenjaminJ.MorganDepartment of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom, The Faraday Institution, Quad One, Harwell Science and Innovation Campus, Didcot, OX11 0RA, United Kingdom0000-0002-3056-823310.21105/joss.05984https://doi.org/10.5281/zenodo.10651128Pythonhttps://joss.theoj.org/papers/10.21105/joss.05984.pdfmolecular dynamics, diffusion, covariance matrix, Bayesian regressiontag:joss.theoj.org,2005:Paper/42112024-01-29T16:38:15Z2024-01-30T08:20:19ZChitin Builder: a VMD tool for the generation of structures of chitin molecular crystals for atomistic simulationsaccepted1.02023-02-15 16:12:05 UTC932024-01-29 16:38:15 UTC920245771DavidMalaspinaInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-5420-9534JordiFaraudoInstitut de Ciencia de Materials de Barcelona (ICMAB-CSIC),Campus UAB Bellaterra, Barcelona, Spain0000-0002-6315-499310.21105/joss.05771https://doi.org/10.5281/zenodo.3274725Tcl, Rich Text Formathttps://joss.theoj.org/papers/10.21105/joss.05771.pdfVMD, chitin polymer structure, molecular dynamics, tcltag:joss.theoj.org,2005:Paper/48562023-12-15T17:52:44Z2023-12-18T20:30:09ZFlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamicsacceptedv1.0.02023-10-18 20:22:59 UTC922023-12-15 17:52:44 UTC820235989MarjanAlbooyehBoise State University, Boise, ID, United States of America0009-0001-9565-3076ChrisJonesBoise State University, Boise, ID, United States of America0000-0002-6196-5274RainierBarrettBoise State University, Boise, ID, United States of America0000-0002-5728-9074EricJankowskiBoise State University, Boise, ID, United States of America0000-0002-3267-141010.21105/joss.05989https://doi.org/10.5281/zenodo.10215501Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05989.pdfmolecular simulation, materials science, molecular dynamics, polymers, HOOMD-bluetag:joss.theoj.org,2005:Paper/44872023-09-05T14:12:36Z2023-09-06T00:01:27ZMolearn: a Python package streamlining the design of generative models of biomolecular dynamicsaccepted2.0.12023-05-17 16:07:52 UTC892023-09-05 14:12:36 UTC820235523SamuelC.MussonDepartment of Physics, Durham University, United Kingdom0000-0002-2189-554XMatteoT.DegiacomiDepartment of Physics, Durham University, United Kingdom0000-0003-4672-471X10.21105/joss.05523https://doi.org/10.5281/zenodo.8284102Pythonhttps://joss.theoj.org/papers/10.21105/joss.05523.pdfmachine learning, molecular dynamics, proteinstag:joss.theoj.org,2005:Paper/43862023-08-10T20:44:28Z2023-08-14T09:04:08ZGMP-Featurizer: A parallelized Python package for efficiently computing the Gaussian Multipole features of atomic systemsacceptedv1.0.02023-04-04 20:31:28 UTC882023-08-10 20:44:28 UTC820235476XiangyunLeiToyota Research Institute, Los Altos, CA, United States of America0000-0002-2333-9205JosephMontoyaToyota Research Institute, Los Altos, CA, United States of America0000-0001-5760-286010.21105/joss.05476https://doi.org/10.5281/zenodo.8170029Python, C++, Chttps://joss.theoj.org/papers/10.21105/joss.05476.pdfParallelization, Machine Learning, Chemistry, Molecular Dynamicstag:joss.theoj.org,2005:Paper/38282023-07-26T13:30:49Z2023-07-27T00:01:46ZAmpTorch: A Python package for scalable fingerprint-based neural network training on multi-element systems with integrated uncertainty quantificationacceptedv0.12022-08-22 16:32:43 UTC872023-07-26 13:30:49 UTC820235035MuhammedShuaibiDepartment of Chemical Engineering, Carnegie Mellon University, United StatesYugeHuDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United States0000-0003-3648-7749XiangyunLeiDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesBenjaminM.ComerDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesMattAdamsDepartment of Chemical Engineering, Carnegie Mellon University, United StatesJacobParasSchool of Physics and School of Computer Science, Georgia Institute of Technology, United StatesRuiQiChenDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesEricMusaDepartment of Chemical Engineering, University of Michigan, United StatesJosephMusielewiczDepartment of Chemical Engineering, Carnegie Mellon University, United StatesAndrewA.PetersonSchool of Engineering, Brown University, United States0000-0003-2855-9482AndrewJ.MedfordDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United States0000-0001-8311-9581ZacharyUlissiDepartment of Chemical Engineering, Carnegie Mellon University, United States0000-0002-9401-491810.21105/joss.05035https://doi.org/10.5281/zenodo.8151492Python, C++, C, G-code, GAPhttps://joss.theoj.org/papers/10.21105/joss.05035.pdfmachine learning interatomic potentials, neural networks, molecular dynamicstag:joss.theoj.org,2005:Paper/41952023-07-06T15:27:41Z2023-07-07T00:01:21ZMembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranesacceptedv0.1.02023-02-07 20:46:18 UTC872023-07-06 15:27:41 UTC820235380AmiraliHosseinEunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America0000-0002-2580-3577AlexanderJ.SodtEunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States of America0000-0002-5570-821210.21105/joss.05380https://doi.org/10.5281/zenodo.8084178Juliahttps://joss.theoj.org/papers/10.21105/joss.05380.pdfbiophysics, molecular dynamics, lipid membranestag:joss.theoj.org,2005:Paper/32712023-04-22T07:17:47Z2023-04-26T19:28:11ZHylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Pythonacceptedv1.0.32022-01-07 23:14:41 UTC842023-04-22 07:17:47 UTC820234149MortenLedumDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0003-4244-4876ManuelCarrerDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-8777-4310SamiranSenDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-1922-7796XinmengLiDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-6863-6078MicheleCascellaDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0003-2266-5399SigbjørnLølandBoreDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States of America0000-0002-8620-488510.21105/joss.04149https://doi.org/10.5281/zenodo.7839898Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.04149.pdfchemistry, physics, molecular dynamics, coarse-grained, hybrid particle-field