tag:joss.theoj.org,2005:/papers/tagged/molecular%20simulation?page=1Journal of Open Source Software2024-03-26T15:54:37ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48572024-03-26T15:54:37Z2024-03-27T00:01:22ZMold: a LAMMPS package to compute interfacial free energies and nucleation ratesacceptedLAMMPS 20232023-10-20 08:11:09 UTC952024-03-26 15:54:37 UTC920246083AndresR.TejedorYusuf Hamied Department of Chemistry, University of Cambridge, United Kingdom, Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-9437-6169IgnacioSanchez-BurgosCavendish Laboratory, Department of Physics, University of Cambridge, United Kingdom0000-0002-1160-3945EduardoSanzDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-6474-5835CarlosVegaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-2417-9645FelipeJ.BlasLaboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, Spain0000-0001-9030-040XRuslanL.DavidchackSchool of Computing and Mathematical Sciences, University of Leicester, United Kingdom0000-0001-9418-5322NicodemoDi PasqualeDepartment of Chemical Engineering, Brunel University London, United Kingdom, Dipartimento di Chimica Industriale, Università di Bologna, Italy0000-0001-5676-8527JorgeRamirezDepartment of Chemical Engineering, Universidad Politécnica de Madrid, Spain0000-0002-8946-3786JorgeR.EspinosaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-9530-265810.21105/joss.06083https://doi.org/10.5281/zenodo.10843863C++https://joss.theoj.org/papers/10.21105/joss.06083.pdfLAMMPS, Molecular simulations, Phase Transitions, Nucleation theorytag: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/47172024-02-07T21:21:42Z2024-02-14T14:53:20ZCLEAVING: a LAMMPS package to compute surface free energiesacceptedv1.0.02023-08-24 09:40:12 UTC942024-02-07 21:21:42 UTC920245886NicodemoDi PasqualeDepartment of Chemical Engineering, Brunel University London, United Kingdom, (Current affiliation) Department of Industrial Chemistry, University of Bologna, Italy0000-0001-5676-8527RuslanDavidchackDepartment of Mathematics, University of Leicester, United Kingdom0000-0001-9418-5322LorenzoRovigattiDepartment of Physics, Sapienza University of Rome, Italy, CNR-ISC UoS Sapienza, Rome, Italy0000-0001-5017-282910.21105/joss.05886https://doi.org/10.5281/zenodo.10567702C++, Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.05886.pdfLAMMPS, Molecular simulations, Phase Transitionstag: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/44572023-11-21T16:27:28Z2023-11-22T08:46:01ZQMCTorch: a PyTorch Implementation of Real-Space Quantum Monte Carlo Simulations of Molecular Systemsacceptedv0.3.02023-04-28 08:45:41 UTC912023-11-21 16:27:28 UTC820235472NicolasRenaudNetherlands eScience Center, Science Park 402, 1098 XH Amsterdam, The Netherlands0000-0001-9589-269410.21105/joss.05472https://doi.org/10.5281/zenodo.10122190Pythonhttps://joss.theoj.org/papers/10.21105/joss.05472.pdfDeep Learning, Quantum Chemistry, Monte Carlo, Molecular Systemstag: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/37082023-01-21T16:46:39Z2023-01-22T21:38:20ZoxDNA: coarse-grained simulations of nucleic acids made simpleacceptedv3.2.22022-07-07 09:39:51 UTC812023-01-21 16:46:39 UTC820234693ErikPoppletonSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of America0000-0002-5146-5970MichaelMatthiesSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of AmericaDebeshMandalDepartment of Materials, Imperial College London, United KingdomFlavioRomanoDipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, ItalyPetrŠulcSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of America0000-0003-1565-6769LorenzoRovigattiDepartment of Physics, Sapienza University of Rome, Italy, CNR-ISC UoS Sapienza, Rome, Italy0000-0001-5017-282910.21105/joss.04693https://doi.org/10.5281/zenodo.7556035Python, C, Cythonhttps://joss.theoj.org/papers/10.21105/joss.04693.pdfC++, DNA, DNA nanotechnology, Molecular simulationstag: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-process