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  2. Algodoo - Wikipedia

    en.wikipedia.org/wiki/Algodoo

    Algodoo (/ ˌ æ l ɡ ə ˈ d uː /) is a physics-based 2D freeware sandbox from Algoryx Simulation AB (known simply as Algoryx) as the successor to the popular physics application Phun. It was released on September 1, 2009 and is presented as a learning tool, an open-ended computer game, an animation tool, and an engineering tool.

  3. Desmond (software) - Wikipedia

    en.wikipedia.org/wiki/Desmond_(software)

    Desmond can also be used to perform absolute and relative free energy calculations (e.g., free energy perturbation). Other simulation methods (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.

  4. NAMD - Wikipedia

    en.wikipedia.org/wiki/NAMD

    Together with Visual Molecular Dynamics (VMD) and QwikMD, [5] NAMD's interface provides access to hybrid QM/MM simulations in an integrated, comprehensive, customizable, and easy-to-use suite. [ 6 ] NAMD is available as freeware for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.

  5. Comparison of software for molecular mechanics modeling

    en.wikipedia.org/wiki/Comparison_of_software_for...

    Free open source: ms-2.de: OpenMM: No No Yes Yes Yes Yes No Yes Yes High Performance MD, highly flexible, Python scriptable Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page ...

  6. GROMACS - Wikipedia

    en.wikipedia.org/wiki/GROMACS

    GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide.

  7. Computational chemistry - Wikipedia

    en.wikipedia.org/wiki/Computational_chemistry

    Molecular dynamics (MD) use either quantum mechanics, molecular mechanics or a mixture of both to calculate forces which are then used to solve Newton's laws of motion to examine the time-dependent behavior of systems. The result of a molecular dynamics simulation is a trajectory that describes how the position and velocity of particles varies ...

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  9. Ragdoll physics - Wikipedia

    en.wikipedia.org/wiki/Ragdoll_physics

    Ragdoll physics is a type of procedural animation used by physics engines, which is often used as a replacement for traditional static death animations in video games and animated films. As computers increased in power, it became possible to do limited real-time physical simulations , which made death animations more realistic.