tag:joss.theoj.org,2005:/papers/tagged/molecular-dynamics-simulationJournal of Open Source Software2024-02-19T16:19:20ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/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/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/42062023-04-17T08:01:50Z2023-04-18T00:02:31ZSolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulationsacceptedv0.2.02023-02-14 19:07:27 UTC842023-04-17 08:01:50 UTC820235183OrionArcherCohenMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0003-3940-2456HugoMacdermott-OpeskinAustralian National University, Australia0000-0002-7393-7457LaurenLeeMaterials Science Division, Lawrence Berkeley National Laboratory, United States of AmericaTingzhengHouInstitute of Materials Research, Shenzhen International Graduate School, Tsinghua University, China0000-0002-7163-2561KaraD.FongMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0002-0711-097XRyanKingsburyEnergy Storage & Distributed Resources Division, Lawrence Berkeley National Laboratory, United States of America0000-0002-7168-3967JingyangWangMaterials Science Division, Lawrence Berkeley National Laboratory, United States of America0000-0003-3307-5132KristinA.PerssonDepartment of Materials Science, University of California, United States of America, Molecular Foundry, Lawrence Berkeley National Laboratory, United States of America0000-0003-2495-550910.21105/joss.05183https://doi.org/10.5281/zenodo.7806199Pythonhttps://joss.theoj.org/papers/10.21105/joss.05183.pdfpython, chemistry, electrolytes, molecular dynamics, solvation structuretag:joss.theoj.org,2005:Paper/36182022-09-22T11:56:28Z2022-09-23T00:01:07ZXponge: A Python package to perform pre- and post-processing of molecular simulationsacceptedv1.2.5.142022-05-22 11:06:01 UTC772022-09-22 11:56:28 UTC720224467YijieXiaCollege of Chemistry and Molecular Engineering, Peking University, China0000-0002-7931-4015YiQinGaoCollege of Chemistry and Molecular Engineering, Peking University, China10.21105/joss.04467https://doi.org/10.5281/zenodo.7073359Pythonhttps://joss.theoj.org/papers/10.21105/joss.04467.pdfmolecular modelling, molecular simulation, molecular dynamics, pre-process and post-processtag:joss.theoj.org,2005:Paper/31972022-01-06T17:19:17Z2022-01-07T00:02:00Zphysical_validation: A Python package to assess the physical validity of molecular simulation resultsacceptedv1.02021-11-30 09:51:45 UTC692022-01-06 17:19:17 UTC720223981PascalT.MerzDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America0000-0002-7045-8725Wei-TseHsuDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of AmericaMattW.ThompsonDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of AmericaSimonBoothroydBoothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London, United KingdomChrisC.WalkerDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of AmericaMichaelR.ShirtsDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309, United States of America0000-0003-3249-109710.21105/joss.03981https://doi.org/10.5281/zenodo.5815657Pythonhttps://joss.theoj.org/papers/10.21105/joss.03981.pdfmolecular simulation, molecular dynamics, molecular mechanics, statistical mechanics, physical validationtag:joss.theoj.org,2005:Paper/28382021-09-19T14:39:23Z2021-09-27T18:10:01ZbuildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parametersacceptedv1.5.02021-07-08 10:19:44 UTC652021-09-19 14:39:23 UTC620213521HubertSantuzCNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, F-75005 Paris, France, Institut de Biologie Physico-Chimique–Fondation Edmond de Rothschild, PSL Research University, Paris, France0000-0001-6149-9480AmélieBacleLaboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, F-86000 Poitiers, France0000-0002-3317-9110PierrePoulainUniversité de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France0000-0003-4177-3619PatrickF.j.FuchsSorbonne Université, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), F-75005 Paris, France, Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France0000-0001-7117-994X10.21105/joss.03521https://doi.org/10.5281/zenodo.5356246Pythonhttps://joss.theoj.org/papers/10.21105/joss.03521.pdfpython, molecular-dynamics-simulation, order-parameters, lipids, united-atomtag:joss.theoj.org,2005:Paper/20462021-03-04T16:01:15Z2021-03-05T00:01:54Zpolypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectoriesaccepted0.82020-09-29 11:38:20 UTC592021-03-04 16:01:15 UTC620212824AdamR.SymingtonDepartment of Chemistry, University of Bath0000-0001-6059-497X10.21105/joss.02824https://doi.org/10.5281/zenodo.4568493Pythonhttps://joss.theoj.org/papers/10.21105/joss.02824.pdfChemistry, Physics, Materials Science, Solid State Chemistry, Simulation, Molecular Dynamics, Monte Carlotag:joss.theoj.org,2005:Paper/17282020-09-25T05:57:10Z2021-02-15T11:30:31ZMetalWalls: A classical molecular dynamics software dedicated to the simulation of electrochemical systemsacceptedversion 12020-06-10 15:15:07 UTC532020-09-25 05:57:10 UTC520202373AbelMarin-LaflècheMaison de la Simulation, CEA, CNRS, Univ. Paris-Sud, UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, FranceMatthieuHaefeleMaison de la Simulation, CEA, CNRS, Univ. Paris-Sud, UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, FranceLauraScalfiSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceAlessandroCorettiDepartment of Mathematical Sciences, Politecnico di Torino, I-10129 Torino, Italy, Centre Européen de Calcul Atomique et Moléculaire (CECAM), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, SwitzerlandThomasDufilsSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceGuillaumeJeanmairetSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceStewartK.ReedSchool of Chemistry, University of Leeds, Leeds, UKAlessandraServaSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceRoxanneBerthinSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceCamilleBaconSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FranceSaraBonellaCentre Européen de Calcul Atomique et Moléculaire (CECAM), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, SwitzerlandBenjaminRotenbergSorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, FrancePaulA.MaddenDepartment of Materials, University of Oxford, Oxford, UKMathieuSalanneMaison de la Simulation, CEA, CNRS, Univ. Paris-Sud, UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France, Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France10.21105/joss.02373https://doi.org/10.5281/zenodo.4040665Pythonhttps://joss.theoj.org/papers/10.21105/joss.02373.pdfFortran, molecular dynamics, electrodes, ionic liquidstag:joss.theoj.org,2005:Paper/15402020-06-03T10:40:49Z2021-02-15T11:30:54Ztaurenmd: A command-line interface for analysis of Molecular Dynamics simulations.acceptedv0.8.92020-03-03 20:18:24 UTC502020-06-03 10:40:49 UTC520202175JoãoM.C.TeixeiraPrevious, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain, Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada0000-0002-9113-062210.21105/joss.02175https://doi.org/10.5281/zenodo.3843326Pythonhttps://joss.theoj.org/papers/10.21105/joss.02175.pdfMolecular Dynamics, Structural Biology, Proteins, DNA, RNA, Biochemistry