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All Topics > Biocomputational Focus > Physics-Based Simulation |
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7 projects in result set.
OpenMM
- OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
<b>NEED HELP?</b> Check out the discussion forums under <a href="https://simtk.org/forums/viewforum.php?f=161">Public Forums</a> and the material from our workshops under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a>.
<b>GET STARTED QUICKLY:</b> Tutorials and sample scripts to run OpenMM are available in the <a href="http://wiki.simtk.org/openmm/VirtualRepository">OpenMM Code Repository</a>.
<b>SOURCE CODE:</b> The source code for OpenMM is available under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a> and also from the <a href="http://www.github.com/SimTk/openmm">Github Source Code Repository</a>.
<b>BENCHMARKS:</b> A collection of <a href="http://wiki.simtk.org/openmm/Benchmarks">benchmarks</a> is available to show the performance of OpenMM simulating a variety of molecular systems.
<b>CITING OPENMM:</b> Any work that uses OpenMM should cite the papers listed on the <a href="https://simtk.org/project/xml/publications.xml/?group_id=161">Publications</a> page. | |
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Registered: 2006-11-16 18:27 |
Simbody: Multibody Physics API
- This project is a SimTK toolset providing general multibody dynamics capability, that is, the ability to solve Newton's 2nd law F=ma in any set of generalized coordinates subject to arbitrary constraints. (That's Isaac himself in the oval.) Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results.
Simbody uses an advanced Featherstone-style formulation of rigid body mechanics to provide results in Order(<em>n</em>) time for any set of <em>n</em> generalized coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait, robotics, avatars, and animation. Simbody can also be used in real time interactive applications for biosimulation as well as for virtual worlds and games.
This toolset was developed originally by Michael Sherman at the Simbios Center at Stanford, with major contributions from Peter Eastman and others. Simbody descends directly from the public domain NIH Internal Variable Dynamics Module (IVM) facility for molecular dynamics developed and kindly provided by Charles Schwieters. IVM is in turn based on the spatial operator algebra of Rodriguez and Jain from NASA's Jet Propulsion Laboratory (JPL), and Simbody has adopted that formulation.
<b>SOURCE CODE:</b> Simbody is distributed in source form. The source code is maintained at <a href="https://www.github.com/simbody">GitHub</a>. You can get a zip of the latest stable release <a href="https://github.com/simbody/simbody/releases">here</a>, then build it on your Windows, Mac OSX, or Linux machine (you will need CMake and a compiler).
You can also clone the git repository and build the latest development version <a href="https://github.com/simbody/simbody">here</a>; the repository URL is https://github.com/simbody/simbody.git. If you would like to contribute bug fixes, new code, documentation, examples, etc. to Simbody (and we hope you will!), please fork the repository on GitHub and send pull requests.
If you are new to git, you may want to start with GitHub's <a href="https://help.github.com/categories/54/articles">Bootcamp tutorial</a>. | |
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Registered: 2005-07-26 19:52 |
SimTK Core Toolset (obsolete project)
- Prior to June, 2011 this project was used to distribute the Simbios-developed Simbody and Molmodel packages in the SimTK biosimulation toolkit. These are now distributed separately from the Simbody and Molmodel projects (https://simtk.org/home/simbody, https://simtk.org/home/molmodel). Please use those projects instead of this one.
The other major component of SimTK is the GPU-accelerated molecular dynamics package OpenMM, see https://simtk.org/home/openmm if you are interested.
<b>The text below refers to the pre-June, 2011 packaging and has been superseded as described above.</b>
<b><i>SimTK Core subprojects</i></b> This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions.
<b><i>SimTK overview</i></b>
SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering.
<b><i>Accessible High Performance Computing</i></b><br/>
We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today's practice, that means commodity multiprocessors and small clusters.
The difference in performance between the best methods and the do-it-yourself techniques most people use can be astounding—easily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as:
Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present.
The resulting pre-built binaries are available for download and immediate use.
<b><i>Citation:</i></b> Any work that uses SimTK Core (including Simbody) should cite the following paper: Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor,Vijay S. Pande, Russ B. Altman, "The Simbios National Center: SystemsBiology in Motion", Proceedings of the IEEE, special issue on Computational System Biology. Volume 96, Issue 8:1266 - 1280. (2008) | |
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Registered: 2006-04-04 20:03 |
ForceBalance : Systematic Force Field Optimization
- ForceBalance is free software for force field optimization.
It facilitates the development of more accurate force fields using a systematic and reproducible procedure.
ForceBalance is highly versatile and can optimize nearly any set of parameters using experimental measurements and/or ab initio calculations as reference data.
<b>SOURCE CODE:</b> For the newest features, visit the GitHub source code repository at https://github.com/leeping/forcebalance.
The SVN repository on the left frame is an outdated archive.
<b>RELEASES:</b> Stable versions of the code updated once every few months. Click "Releases" on the left frame for the most recent release and notes.
<b>CONTACT:</b> Please contact me (Lee-Ping, right frame) if you have questions or comments! | |
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Registered: 2011-12-20 17:04 |
Sensory Components for Simulating Postural Feedback Control in OpenSim
- This project provides software for simulating physiological sensors and postural stability with feedback responses. | |
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Activity Percentile: 0.00 Registered: 2013-04-30 19:36 |
Molmodel: SimTK molecular modeling API
- Molmodel is a programmer’s toolkit for building reduced-coordinate, yet still all-atom, models of large biopolymers such as proteins, RNA, and DNA. You control the allowed mobility. By default, Molmodel builds torsion-coordinate models in which bond stretch and bend angles are rigid while bond torsion angles are mobile. But you can rigidify or free any subsets of the atoms, such as the rigid benzene ring shown here.
Molmodel is a C++ API for biochemist-friendly molecular modeling that extends the Simbody API to simplify construction of high-performance articulated models of molecules. All of the Simbody API is available when using Molmodel and Simbody must be installed and functioning in order to use Molmodel. See https://simtk.org/home/simbody for more information. Read the Simbody User’s Guide for background, installation instructions, and examples.
Molmodel can produce models with dramatically fewer degrees of freedom than a typical molecular model, yet the reduced set of coordinates is still a fully nonlinear basis for molecular motions of any size. Structural searches and optimizations benefit from a much reduced search space, Monte Carlo moves can achieve much higher acceptance rates, and dynamics can proceed with much larger step sizes due to the lower natural frequencies produced by larger moving bodies. Because all the atoms are still present, conventional force fields and implicit solvent models can be used for energy and force computations, and Molmodel can use OpenMM (https://simtk.org/home/openmm) to accelerate those calculations. Alternatively, Molmodel is flexible enough to allow you to design your own force fields. Physics-based, knowledge-based, and special-purpose potentials can be designed and incorporated into your Molmodel model.
While reduced coordinate models have been used succesfully for a variety of purposes (they are ubiquitous in NMR structure refinement, for example), research is needed to determine the best way to model a given molecular system for the particular study at hand. Both the physical properties of a molecular system of interest, and the particular investigation being performed will influence the best choice of model. The point of Molmodel is to enable you or users of your software to perform those studies by providing making it easy to create molecular models with mobility only where you choose to allow it, and then to easily revise those choices.
Molmodel, Simbody, and OpenMM are components of the open source biosimulation toolkit SimTK, developed and supported by the NIH-funded Center for Physics-Based Simulation of Biological Structures at Stanford (http://simbios.stanford.edu). Molmodel was developed originally for SimTK by Christopher Bruns and Michael Sherman, with major contributions from Peter Eastman and Samuel Flores.
<b>NOTE:</b> Prior to the 2.2 release, binaries of Molmodel were bundled with other SimTK Core modules. Those can still be found in the Downloads section of the SimTKcore project, at http://simtk.org/home/simtkcore. | |
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Registered: 2007-03-01 17:33 |
Application for the simulation of the prosthetic gait
- This application has a dataset belonging to macha prosthetic patterns , in which the angle of the socket and prosthetic foot is changed.
It focuses on patients with transtibial amputation and uses opensim in MATLAB libraries to link and generate a model for opensim , based on data captured from a measuring TECHNAID brand. | |
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Registered: 2016-08-24 14:21 |