HHMI is a science philanthropy whose mission is to advance biomedical research and science education for the benefit of humanity. We empower exceptional scientists and students to pursue fundamental questions about living systems. Headquartered in Chevy Chase, MD, HHMI employs more than 3,000 individuals across the United States. In fiscal year 2012, HHMI invested $695 million in U.S. research and provided $78 million in grants and other support for science education.
SimTK ISIM interface a simple Java graphical user interface for running the program ISIM. ISIM is package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD (http://mccammon.ucsd.edu/isim/). The version of ISIM used is available in the ISIM project on simtk.org.
Keywords: grand canonical ensemble, monte carlo
OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations.
Keywords: Gromacs, molecular dynamics interface
This project creates an easier to use python API for the SimTK core multibody mechanics simulation tool kit.
Keywords: internal coordinates, multibody dynamics, python, simtk core, torsion coordinates
Sequoia is a command-line tool for the alignment of molecular protein sequences and atomic structures. It is not exactly simulation, but it needs a stable home. I wrote it over the past 10 years, and some users have started to complain that my home server is no longer reliably available.
This project is a collection of Java classes for use in constructing Java applications that use the simulation tool kit.
SimTK ToRNADo is a dynamic visualization tool for coarse grain (lumped) representations of RNA and/or protein structure. By shifting the focus from individual atoms to higher order structures, such as double helical duplexes, the scientist's attention is naturally focuses toward a larger scale. Biologists will be able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another.
Keywords: RNA, RNA secondary structure