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11 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 |
MMB (MacroMoleculeBuilder)
- MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein and DNA and protein as well as RNA. You can use MMB for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications limited mostly by your imagination.
MMB was written by Samuel Coulbourn Flores at the Stanford Simbios Center. It is currently maintained by the same person, now as Dean of the Swedish National Graduate School in Medical Bioinformatics, based at Stockholm University, Sweden. | |
Registered: 2008-12-05 00:15 |
Musculoskeletal Model of the Lumbar Spine
- The work here features a number of different OpenSim models of the lumbar spine developed to study lumbar kinematics and dynamics.
Briefly, the models consist of the following bodies:
# rigid pelvis and sacrum
# five lumbar vertebrae (separated by joints with three rotational degrees of freedom)
# torso (thoracic spine + ribcage)
The motion of the individual joints are defined using constraint functions specifying the motion of the lumbar vertebra as functions of the net lumbar motion (flexion-extension, lateral bending and axial rotation). Future models will incorporate joints with stiffness properties to more accurately mimic the action of the intervertebral joints.
The most complex of these models also feature the 238 muscle fascicles associated with the 8 main muscle groups of the lumbar spine necessary to study the contribution of the lumbar spinal musculature to spinal motion. Simpler models incorporating two and seven of the main muscle groups of the lumbar spine are provided as well for completeness.
Read more about the model in the paper, freely downloadable at http://link.springer.com/article/10.1007%2Fs10237-011-0290-6.
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September 2011 Addendum
Click on the "Downloads" link to the left for downloads related to more recent work.
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September 2012 Addendum
The Constrained Lumbar Spine Model does not require any of the files uploaded after the creation of the Constrained Lumbar Spine Model project. The .vtp files (and descriptions) are included here for the benefit of those of you who wish to create your own model that has origins shifted to the center of the bones since this typically saves a number of transformations. Many apologies for any confusion(!).
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March 2014 Addendum
(1)
This model was build with OpenSim 2+. Version 3+ will not allow you to use periods (.) in your variable names. Unfortunately, a bunch of the variables used (muscles mainly) have periods in the names so it will throw an error if you try and run it in OpenSim version 3+. To fix this, either use version 2+, OR, rename the variables appropriately.
(2)
We have all graduated and are no longer actively working on this project (we haven't been working on it since the end of 2011 actually). At this point, you probably know more than us about OpenSim so we apologize in advance if our support is subpar.
(3)
The complex mode is not meant to be run straight out of the box. It has almost 250 muscles after all and unless you have a super computer, running CMC, or FD on it is going to bring up the rainbow ball of death on your computer.
Rather, it's meant to be a reference for those of you who intend to build up your own model. My advice would be to start with the simple 4 fascicle model, get it to work, then incrementally build up from there using the parameters provided in our model as a starting point. Copy-Paste is your friend here. :)
(4)
If this is your very first OpenSim project, I strongly _strongly_ *strongly* suggest that you go through the examples provided with the OpenSim version you just downloaded and understand how they work. This will save you months of pain down the road. | |
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Activity Percentile: 79.39 Registered: 2010-11-04 02:25 |
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 |
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 |
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 |
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 |
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 |
A Coarse-Grained Physical Model for RNA
- This project aims to develop a coarse-grained (CG) model for RNA at the functional group, residue as well as secondary structure level. In the functional group-based model, each sugar ring, phosphate backbone and base group will be represented as a CG particle. The “shape” of the particle is described by the anisotropic Gay-Berne function. Point multipoles are placed at the center and selected off-center sites. This model has been shown successful in describing hydrogen-bonded molecular liquids (see publication). | |
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Activity Percentile: 0.00 Registered: 2006-09-19 17:35 |
LAPACK linear algebra library (with BLAS)
- This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. We make use of ATLAS to generate "hand tuned" BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. We pre-build on all these platforms and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines.
Our download page provides libraries that are specifically tuned for your hardware platform -- come and get 'em. The project also provides example programs, documentation and regression tests. | |
Activity Percentile: 0.00 Registered: 2005-08-22 19:47 |
Anatomicaly-based 3D models of the middle ear and the inner ear
- The OtoBiomechanics Group at Stanford is developing three-dimensional and multiscale bio-computational models of the middle ear and the inner ear and their applications to understanding disease processes and interventions.
This project is a collection of code that simulates the biomechanics of the cochlea and the middle ear. At the core is FAST4. This is a program for calculating axisymmetric shells of revolution. FAST4 uses asymptotic methods for calculations, which are orders of magnitude faster than other methods including the finite element approach. The interface to FAST4 is built using MATLAB or Mathematica. | |
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Activity Percentile: 0.00 Registered: 2006-06-05 05:53 |