Simbios held a workshop to introduce programmers and modelers to the essential features of the SimTK toolkit, as well as to new and more advanced features available through the release of SimTK 1.5 in early August.
What is SimTK? SimTK provides a one step install of many components needed for the simulation of biological structures including: linear algebra, root finding, vector systems, rotations and the expression of directions, optimization, numerical differentiation and integration, Molmodel: the SimTK molecular modeling library, as well as Simbody: a system for rigid multi-body dynamics.
On the first day:
- Learn about Simbody, SimTK's multibody dynamics engine, and how to use it to perform simulations
- Use SimTK to write a program simulating a pendulum and quickly be able to simulate a double pendulum and more generally a system of interacting rigid bodies
- Learn how to apply arbitrary forces to your system and how to use mobilizers and constraints
- Write a simulation using constraints
- Learn about the basic and advanced integrators available through SimTK
- Understand and learn to take advantage of the architecture of SimTK and Simbody including systems, subsystems and events in your simulatio
The second day was devoted to advanced topics and application areas. Two separate sessions were run. One was devoted to Molmodel, for students interested in applying SimTK for molecular applications, while the other session covered advanced topics, such as how to write new subsystems and mobilizers.
Click here for detailed agenda.
Preparing for the Workshop
Before attending the workshop, attendees
were expected to have:
- Installed release 1.5 on their laptops (Windows, Linux and Mac are supported) and run the test programs to verify the installation
- Downloaded the examples provided, compiled and verified that they can compile and run at least some of them.
SimTK 1.5 Features
Our 1.5 release has several new features, including:
- Tighter integration with OpenSim
- Significant improvement in performance, including utility classes for multithreading calculations
- The ability to fit splines to data
- An API for creating new MobilizedBody types
- The ability to calculate mobilizer reaction forces
- Ability to view molecular simulations live in VMD
- Improved support for loading PDB files
Documentation, slides and videos of the workshop sessions can be
downloaded from the Documents section of http://simtk.org/home/simtkcore.