AMOEBA's polarizable force field now integrated with OpenMM
Many have long hoped that molecular dynamics calculations—the computation of how molecules move and interact with other molecules—would revolutionize the world of synthetic chemistry,...
Sep, 01, 2011
OpenMM provides a common interface for doing MD simulations on GPUs
Over the last three years, the lab of Vijay Pande, PhD, at Stanford University has optimized their molecular dynamics (MD) algorithms to take advantage of the fast computing that’s possible...
Jul, 01, 2008
Kim Branson of Vertex Pharmaceuticals uses OpenMM as the GPU accelerator for Yank, a program for quickly estimating molecular binding affinities that he’s building with collaborators from Pande’s lab.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Kim Branson, PhD, a research scientist in the modeling and simulation group at Vertex...
Oct, 01, 2009
Notre Dame’s Jesus Izaguirre collaborates with Simbios to increase the time scales of protein folding simulations with OpenMM. Why team up with Simbios? Because “they are working on exciting problems and have good people,” he says.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Jesus Izaguirre, PhD, associate professor of computer science and engineering at the...
Oct, 01, 2009
Erik Lindahl of Stockholm University uses OpenMM to speed up molecular simulations of membrane proteins and takes inspiration from Simbios’ professional approach to software development as he continues developing and maintaining GROMACS.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Simbios provides two key benefits to Erik Lindahl, PhD, associate professor of...
Oct, 01, 2009
How Simbios' state-of-the-art software tools are contributing to high-impact biomedical research
Simbios began with a simple idea: that physics-based simulation of biological structures at all scales could benefit from a
unified tool-building effort.
At the same time, the thinking went,...
Oct, 01, 2009
A unique opportunity to build both flexibility and high performance into a piece of software.
OpenCL is a cross-platform language for doing general purpose computation on graphics processing units (GPUs) and other massively parallel architectures. One of its most interesting features is the...
Apr, 01, 2010
Using molecular dynamics (MD) software, scientists can simulate molecular movement to study biological phenomena that currently cannot be observed experimentally.
But the value of MD...
Jul, 01, 2009
When you step on the gas pedal, you expect acceleration (and lots of it). Stomp on the brake to come safely to a stop in the rain. Finger the power-assisted steering wheel and the car obeys. Make a...
Oct, 01, 2009
From hardened software to scientific productivity, the NCBCs have changed the landscape for biomedical computing. What will happen when their funding expires?
It has been eight years since the National Institutes of Health (NIH) funded the first National Centers for Biomedical Computing (NCBCs). With two or three years remaining in the program (...
Oct, 19, 2012
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