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All Topics > Biocomputational Focus > Physics-Based Simulation |
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19 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 |
Statistical analysis of conformational ensembles
- This project provides computational tools and methods to analyze conformational ensembles of biomolecules, as well as their assemblies, such as those obtained from molecular simulations.
(A) PROTEINS: The molecular understanding of the functional regulation of proteins requires assessment of various states, including active and inactive states, as well as their interdependencies. For several proteins, their various states can be distinguished from each other on the basis of their minimum energy 3D structures. For many other proteins, like GPCRs, PDZ domains, nuclear transcription factors, heat shock proteins, T-cell receptors and viral attachment proteins, their states can be distinguished categorically from each other only when their finite-temperature conformational ensembles are considered alongside their minimum-energy structures. We are developing tools/methods for:
(A1) Direct comparison of conformational ensembles - The traditional approach to compare two or more conformational ensembles is to compare their respective summary statistics. This approach is, however, prone to artifactual bias, as data is compared after dimensionality reduction. The proper way to compare ensembles is to compare them directly with each other and prior to any dimensionality reduction. g_ensemble_comp is a tool we have developed that does just that and reports the difference between ensembles in terms of a true metric defined by the zeroth law of thermodynamics.
(A2) Prediction of allosteric signaling networks - method under development.
(B) LIPID MEMBRANES: The surface area of a lipid bilayer is related fundamentally to many other observables, such as thermal phase transitions and domain formation in mixed lipid bilayers. We have developed g_tessellate_area to compute the 3D surface area of a bilayer using Delunay tessellation. | |
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Activity Percentile: 94.66 Registered: 2015-09-15 17:52 |
Data for Exacycle GPCR paper on cloud-based simulations
- This project provides links to the GPCR trajectory data used for the analysis in the paper on cloud-based simulations on Google Exacycle. The data is available for download and can be used freely by anyone. | |
Activity Percentile: 66.03 Registered: 2013-12-13 19:27 |
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 |
Ligand Binding in Beta1-Adrenergic Receptor MD Model
- This project is a collection of molecular dynamics trajectories modeling the turkey B1AR crystal structure (PDBID: 2VT4 and 2Y02) in an explicit membrane and solvent model (using Maestro and Desmond by Schrodinger). The protein was modeled with and without thermostabilizing point mutations (from crystalization) reversed, and in several ligand conditions: without a ligand, with antagonist cyanopindolol, and agonists carmoterol and isoprenaline. Computational biologists interested in GPCRs can study the small movements of amino acid side chains that lead to activation in these trajectories. | |
Activity Percentile: 0.00 Registered: 2012-07-11 01:53 |
Simulating rare events using a Weighted Ensemble-based string method
- Python implementation of the Weighted Ensemble-based string method that provides an efficient algorithm for sampling equilibrium and non-equilibrium transitions in complex systems. | |
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Activity Percentile: 0.00 Registered: 2012-12-05 21:53 |
Ribosomal translocation with EF-G
- This project aims at providing new insight about RNA translation into protein, focusing on the translocation step induced by Elongation Factor G (EF-G). In the past few years, biologists provided high-resolution structures of key steps of the process. Our goal is to compute a trajectory of the translocation at atomic level using an accurate morphing technique. | |
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Activity Percentile: 0.00 Registered: 2014-07-23 13:04 |
ADPt-Gromacs - Coupling homologous replicas by adaptive position restraints
- We develop an implementation of adaptive position restraints for the GROMACS MD simulation software. The goal is to improve refinement of protein structures. | |
Activity Percentile: 0.00 Registered: 2015-06-28 19:26 |
KGS: Sampling and Characterizing Protein and RNA conformational landscapes
- The Kino-Geometric Sampling (KGS) software suite uses advanced, robotics-inspired algorithms to rapidly explore the conformational landscape of folded proteins, RNA, and their complexes. Combined with powerful statistical techniques, it structurally characterizes collective motions and excited substates from sparse, spatiotemporally averaged data. | |
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Activity Percentile: 0.00 Registered: 2015-12-11 21:41 |
C++ and Python code, distributed computing and OpenMM interfaces for simulations
- please cite: "Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon" (PLOS One 2013)
for any code related to protein-DNA modeling and
"Free Energy Monte Carlo Simulations on a Distributed Network" (Lecture Notes in Computer Science Journal for PARA 2010)
http://link.springer.com/chapter/10.1007%2F978-3-642-28145-7_1
for parallel client-server code, users of additional code should cite this web site. Code is provided as-is with no warranty and examples are provided to illustrate the usage of these modeling techniques with some sample systems. Code is the intellectual property of Luke Czapla, developer and biophysicist. Examples are provided in C/C++ and Python. | |
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Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
Data repository for TIP3P-FB and TIP4P-FB water model parameterization.
- This is a data repository for the parameterization of the TIP3P-FB and TIP4P-FB rigid water models. | |
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Activity Percentile: 0.00 Registered: 2014-03-20 17:22 |
Lead Optimization Mapper (LOMAP)
- This provides tools relating to mapping pharmaceutical lead optimization campaigns. The initial implementation is focused on planning free energy calculations to span a library of inhibitors by computing relative free energies between related inhibitors, but the scope of the mapper will likely expand with time. This toolkit:
- is written in Python
- turns the problem of planning relative free energy calculations within a library into a graph theory problem
- outputs a map of planned calculations
This is written for computational scientists working in the pharmaceutical industry generally, including academia, industry, and elsewhere, who need tools to help plan lead optimization campaigns.
The code is being released under the BSD license and hopefully will be a community effort.
Please contact David Mobley and Shuai Liu if you need any help getting this to work or any clarification on installing, etc.
If you use this, please cite our paper in JCAMD: http://link.springer.com/article/10.1007%2Fs10822-013-9678-y | |
Registered: 2012-06-11 16:22 |
Weighted histogram analysis method with Bayesian bootstrapping
- The free energy (or the potential of mean force) along a set of reaction
coordinates is a central quantity in computational chemistry. Umbrella sampling
combined with weighted histogram analysis method (WHAM) is a powerful tool for
such calculation. Here, I have provided a set of programs to perform WHAM with
Bayesian bootstrapping. The source code for these programs are available for
free under a general public license (GPL). | |
Activity Percentile: 0.00 Registered: 2014-01-26 14:44 |
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 |
PDBManip: PDB (Protein Data Bank) Editor and Manipulator Utility
- PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. While all those programs offer only a few predefined tasks, PDBManip uses AngelScript language which is very similar to C/C++ language, to allow the users to write their own scripts to define editing tasks, although PDBManip contains many useful example scripts. I know that the text-manipulation script languages such as Awk and Perl are available, and many users, uses these to do their works. However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. In this way, proficiency in computer programming, that is a must in using Awk or Perl, is not a barrier. | |
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Registered: 2016-08-06 06:48 |
SBMOpenMM: Structure-based model library for protein simulations in OpenMM
- The library offers flexibility for creating SBM force fields that can be customized to capture different aspects of protein SBM potential energy exploration.
Considering an input structure, the library automatizes the creation of forces to specify it as the only minimum configuration in the potential energy function. Bonds, angles, and torsions are maintained close to their equilibrium configuration, while native contact interactions can form and break using regular or modified Lennard-Jones potentials. This allows complete and local protein unfolding, restricting the interactions only to the evolutionarily relevant chemical contacts and exploring the relevant configurational space of protein folding and function.
Different granularities for the models can be selected as All-heavy-Atom and alpha-carbon representations. These basic models can also be extended to multi-basin potentials employing more than one input configuration. Here, shared native contacts are modeled with special Gaussian functions to allow for more than one equilibrium distance.
The library offers many methods to tailor forcefield parameters and definitions for each force term. Combining these basic methods and force implementations, sbmOpenMM offers an easy setup of a more complex force field definition that can aid in better exploration of different biophysical phenomena. | |
Registered: 2019-10-15 09:48 |
HTMD - High Throughput Molecular Dynamics
- In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.
See more information on <a href="https://www.htmd.org/">https://www.htmd.org</a>.
HTMD Forum: <a href="https://forum.htmd.org/">https://forum.htmd.org</a>
We are also on Github: <a href="https://github.com/Acellera/htmd">https://github.com/Acellera/htmd</a>
Report issues on: <a href="https://github.com/Acellera/htmd/issues">https://github.com/Acellera/htmd/issues</a> | |
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Registered: 2016-05-13 07:45 |