[Simbiosnews] Simbios Update - July 2010

[Joy P. Ku]

Simbios Update.

 

1)      1)  OpenSim Jamboree brings together researchers from around the
world

2)      2)  OpenMM 2.0 enables molecular dynamics acceleration on ATI and
NVIDIA GPUs

3)      3)  AMBER/Sander-compatible interface to OpenMM just released

4)      4)  Special issue from Royal Society Publishing - The virtual
physiological human:  computer simulation for integrative biomedicine

 

  _____  

 

1)      1)  OpenSim Jamboree Brings Together Researchers from Around the
World
The OpenSim Developer Jamboree, an intense working session that brought
together researchers from 14 institutions around the world, was held from
July 12-14.  The OpenSim <http://simtk.org/home/opensim>  software enables
computer modeling and dynamic simulations of  movement. During these three
days, participants worked with the newest version of OpenSim and received
help from the OpenSim team on individual research projects.  Exciting
progress was made on biomechanical research questions and useful plugins
for the OpenSim community.  In addition, participants were introduced to a
Matlab/Simulink interface <http://simtk.org/home/opensim_matlab>  to
OpenSim, developed by Prof. Reinbolt as part of a Simbios seed grant. 

2)       

2)  OpenMM 2.0 Enables Molecular Dynamics Acceleration on ATI and NVIDIA
GPUs
Simbios is excited to announce the release of OpenMM 2.0,  a major update
of this library for accelerating molecular dynamics. This version supports
accelerated calculations on NVIDIA GPU cards (using either CUDA or
OpenCL), as well as ATI GPU cards (using OpenCL).  It also includes
pressure coupling, more custom force types, and significant performance
increases. You can download OpenMM  from http://simtk.org/home/openmm.
OpenMM 2.0 has been made available to GROMACS users (via
OpenMM-Accelerated GROMACS) and to AMBER users (via an
AMBER/Sander-compatible interface to OpenMM, available at
http://simtk.org/home/sander_openmm).

5)       

6)       <http://simtk.org/home/opensim> 3)  AMBER/Sander-compatible
interface to OpenMM Just Released

7)      AMBER users are now able to use the power of OpenMM to run
accelerated molecular dynamics with their existing Sander input files.
The code for the AMBER/Sander-compatible interface to OpenMM and exciting
benchmark numbers for systems including the villin headpiece, lambda
repressor, and alpha spectrin are available for download from
http://simtk.org/home/sander_openmm <https://simtk.org/home/sander_openmm>
.

 

 <https://simtk.org/home/sander_openmm> 4)  Special issue from Royal
Society Publishing - The virtual physiological human:  computer simulation
for integrative biomedicine

Simbios EU collaborators have been actively involved in a special issue
from Royal Society Publishing on "The virtual physiological human:
computer simulation for integrative biomedicine."  See
http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-h
uman.xhtml for further details.   All articles in this double issue (along
with all content back to 1665) are free to access up until the end of July
2010.

 <https://simtk.org/home/sander_openmm>  

 <https://simtk.org/home/sander_openmm>
______________________________________________________

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> Joy P. Ku

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> Director of Dissemination

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> Simbios, Stanford University

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> (W) 650.736.8434 

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> (F) 650.723.7461

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> Email:  joyku at stanford.edu

 
<http://rsta.royalsocietypublishing.org/site/issues/virtual-physiological-
human.xhtml> Website:  http://simbios.stanford.edu

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