Free Molecular Modeling Software Mac

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Three dimensional molecular model of an all-carbon tubular fullerene.
  1. Free Molecular Visualization Software
  2. Molecular Simulation Software
  3. Image Editing
  • Jmol is one of the best chemical structure drawing software that is based on open-source java viewer. Jmol is an interactive and powerful web browser applet with featured for crystals, chemicals, biomolecules, and materials. This software can conveniently run on Windows, Mac OS X, and Linux/Unix systems.
  • Free, open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications (hosts, i.e. Blender, Cinema4D and Maya 2011) to provide simultaneous access the capabilities of all of the systems.
  • MolView is an intuitive, Open-Source web-application to make science and education more awesome!
  • To visual your own pdb structure right click and chose open with (Yasara). This free program is part of a more extensive molecular modeling package. RasMol is software for looking at molecular structures. It is very fast: rotating a protein or DNA molecule shows its 3D structure.

This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics[1] and quantum mechanics.

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Free, Open Source: Easy to install and all source code and documentation is.

  • Aionics.io[2] - a powerful platform for nanoscale modelling
  • Atomistix ToolKit and Virtual NanoLab[3]
  • CST Studio Suite[4]
  • Deneb[5] – graphical user interface (GUI) for SIESTA, VASP, QE, etc., DFT calculation packages
  • Exabyte.io[6] - a cloud-native integrated platform for nanoscale modeling, supporting simulations at multiple scales, including Density Functional Theory and Molecular Dynamics
  • JCMsuite – a finite element analysis software for simulating optical properties of nanostructures
  • LAMMPS – Open source molecular dynamics code
  • MAPS - Graphical user interface to build complex systems (nanostructures, polymers, surfaces...), set up and analyze ab-initio (Quantum Espresso, VASP, Abinit, NWChem...) or classical (LAMMPS, Towhee) simulations
  • nanoHUB allows simulating geometry, electronic properties and electrical transport phenomena in various nanostructures
  • Ninithi – carbon nanotube, graphene, and Fullerene modelling software
  • Nanoengineer-1[7] – developed by company Nanorex, but the website doesn't work, may be unavailable
  • NEMO 3-D[8] – enables multi-million atom electronic structure simulations in empirical tight binding; open source; an educational version is on nanoHUB and Quantum Dot Lab[9]
  • Nanotube Modeler[10]
  • Materials Design MedeA[11]
  • Materials Square[12] - a cloud-based materials simulation web platform, provides GUI for Quantum Espresso, LAMMPS, and Open Calphad
  • MBN Explorer and MBN Studio[13][14]
  • MD-kMC[15]
  • PARCAS[16][17][18] – Open source molecular dynamics code
  • SAMSON: interactive carbon nanotube modeling[19] and simulation[20]
  • TubeASP[21]
  • Tubegen[22]
  • Wrapping[23]

See also[edit]

References[edit]

Free Molecular Modeling Software Mac
  1. ^Huhtala, Maria; Kuronen, Antti; Kaski, Kimmo (2002). 'Carbon nanotube structures: molecular dynamics simulation at realistic limit'(PDF). Computer Physics Communications. 146 (1): 30. Bibcode:2002CoPhC.146...30H. doi:10.1016/S0010-4655(02)00432-0. Archived from the original(PDF) on 27 June 2008.
  2. ^Aionics
  3. ^Brandbyge, Mozos, Ordejón, Taylor and Stokbro (2002). 'Density-functional method for non-equilibrium electron transport'. Physical Review B. 65 (16): 165401. arXiv:cond-mat/0110650. Bibcode:2002PhRvB..65p5401B. doi:10.1103/PhysRevB.65.165401.CS1 maint: multiple names: authors list (link)
  4. ^CST Studio Suite
  5. ^Deneb
  6. ^Exabyte
  7. ^Nanoengineer-1Archived 2015-08-01 at the Wayback Machine
  8. ^NEMO 3-D
  9. ^Quantum Dot Lab
  10. ^Nanotube Modeler
  11. ^Materials Design MedeA
  12. ^Materials Square
  13. ^I.A. Solov'yov; A.V. Korol; A.V. Solov'yov (2017). Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer. Springer International Publishing. ISBN978-3-319-56085-4.
  14. ^'MBN Explorer and MBN Studio software'.
  15. ^MD-kMC
  16. ^Nordlund, K.; Ghaly, M.; Averback, R. S.; Caturla, M.; Diaz de la Rubia, T.; Tarus, J. (1998-04-01). 'Defect production in collision cascades in elemental semiconductors and fcc metals'. Physical Review B. 57 (13): 7556–7570. Bibcode:1998PhRvB..57.7556N. doi:10.1103/PhysRevB.57.7556.
  17. ^Ghaly, Mai.; Nordlund, Kai.; Averback, R. S. (1999). 'Molecular dynamics investigations of surface damage produced by kiloelectronvolt self-bombardment of solids'. Philosophical Magazine A. 79 (4): 795–820. Bibcode:1999PMagA..79..795G. doi:10.1080/01418619908210332. ISSN0141-8610.
  18. ^Nordlund, K. (1995). 'Molecular dynamics simulation of ion ranges in the 1–100 keV energy range'. Computational Materials Science. 3 (4): 448–456. doi:10.1016/0927-0256(94)00085-q. ISSN0927-0256.
  19. ^SAMSON Element: Nanotube creator
  20. ^SAMSON Element: Brenner interaction model
  21. ^TubeASP
  22. ^Tubegen
  23. ^Wrapping
Free Molecular Modeling Software Mac
Retrieved from 'https://en.wikipedia.org/w/index.php?title=List_of_software_for_nanostructures_modeling&oldid=997197606'
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
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NAMD and VMD are part of the team winning the 2020 ACM Gordon Bell Special Prize for high performance computing-based COVID-19 research, for the paper AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics, presented at Supercomputing 2020, Nov 18, 2020.

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Modern computers include a massively parallel graphicsprocessing unit (GPU) designed to perform geometry and lightingcalculations at blistering speeds.State of the art GPUs can perform 0.5 teraFLOPS with theirhundred cores.The tremendous computational power of GPUs was untapped by scientific computations because it could only beaccessed with difficulty until now.As reported in the Journal of Computational Chemistry, recent advancesallowing GPUs to be used for general purpose computing haveboosted the performance of a number of molecular modeling applications, includingNAMD simulations and VMD electrostatic potential calculations.The accelerated versions of theseapplications run five to one hundred times faster than on the bestCPU-based hardware, allowing a single desktop computer equipped with a GPU to provide processing power equivalentto an entire, large computing cluster. More information on GPU acceleration of molecular modeling applications is providedhere.
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Molecular representations
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GPU-accelerated computing
Interactive molecular dynamics
Programs that use VMD
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VMD citation list (37,000 as of Mar'21)

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VMD 1.9.3 (MacOS X, Unix, Windows)
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Free Molecular Visualization Software

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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics, IJHPCA, 2021
Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales, J. Par. Comp. 2021
NAMD and VMD part of the team winning the ACM COVID-19 Gordon Bell Prize for 2020
The Coronavirus Unveiled, VMD visualizations of SARS-CoV-2, NYT, 2020
Scalable molecular dynamics on CPU and GPU architectures with NAMD, JCP, 2020
VMD test builds for MacOS X 10.15 'Catalina' (April 24, 2020)
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An Accessible Visual Narrative for the Primary Energy Source of Life from the Fulldome Show Birth of Planet Earth, 1st Place Winner, SC'19 Viz. Showcase
Chromatophore VR demo (VMD + Unreal Game Engine) shown in NVIDIA booth at SC'16
Example VMD VR/3-D YouTube videos
Chemical Visualization of Human Pathogens: the Retroviral Capsids, Finalist, SC'15 Viz. Showcase
Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail, 1st Place Winner, SC'14 Viz. Showcase
VMD movie gallery on YouTube
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VMD running in the NanoDome at Temple University

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VMD User Survey Results
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