NAMD and VMD at SC2001
Theoretical Biophysics (TBG) and Sun Microsystems Demo
Title:
NAMD and VMD: Interactive Molecular Dynamics Simulation
Location:
Sun booth
Investigators:
Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers:
James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG)
Presenter:
Jim Phillips, TBG
Contacts:
Ferhat Hatay, Eugene Loh: Sun Microsystems
TBG Equipment:
Spaceball, Phantom haptic, portland laptop,
transportation to Denver by Bruce Loftis.
TBG Support:
Setup and operation of TBG equipment and software during expo.
What will be demonstrated:
IMD simulations will be performed using NAMD on two
12 processor SunFire 6800s with Sun's new interconnect and
ClusterTools 4.0 MPI parallel communication software.
The interactive simulation rates and parallel scalability of NAMD
will be directly highlighted by the IMD simulations demonstrated
at the show.
VMD will be demonstrated on a SunBlade 1000 equipped with
Elite3D-m6 graphics and UltraSPARC-III processors using
Spaceball and haptic input devices for finer 3-D positioning and
steering.
The haptic device will be driven by a dedicated laptop running
the UNC VRPN software.
NAMD and VMD are developed by the Theoretical Biophysics Group at the
University of Illinois. NAMD and VMD development is supported by
the NIH National Center for Research Resources.
"If I could just get my hands on that protein!" Single molecule
manipulation techniques like atomic force microscopy have brought us
closer to this frequently expressed wish. These techniques, however,
do not "see" the atomic level detail needed to relate mechanism to
protein architectures. True, computational methods do illuminate the
elusive protein structures, but are limited to static structures, or
trajectories yielded by weeks-long simulations. Now, with
the advent of high-performance computing, interactive
manipulation of molecular dynamics simulations has become a reality.
Linking advanced
molecular graphics
with ongoing
molecular dynamics
simulations, and utilizing a
haptic device
to connect forces from a
user's hand with forces in the simulation, researchers can interact
with "live" proteins. The new methodology is described in a recent
publication
and the figure shown here demonstrates a Cl- ion being
pulled through a gramicidin A channel
(see a 3.8mb Streaming Video).
Theoretical Biophysics (TBG) Talk in PSC Booth
Title:
NAMD: Scalable Molecular Dynamics
Location and Time:
PSC booth, 2pm, Thursday November 15, about 20 minutes.
Investigators:
Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers:
James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG),
David O'Neal (NCSA and PSC)
Presenter:
Jim Phillips, TBG
Contacts:
Ralph Roskies at PSC
Abstract:
NAMD is a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems. NAMD was used
on TCS1 to perform a 327,000 atom simulation of the ATP-synthase F1 unit.
NAMD and VMD are developed by the Theoretical Biophysics Group at the
University of Illinois. NAMD and VMD development is supported by
the NIH National Center for Research Resources.
Theoretical Biophysics (TBG) and NCSA Itanium Cluster and Display Wall Demo
Title:
NAMD and VMD: Live Molecular Dynamics Simulation and Visualization
on NCSA Itanium Linux Cluster and Tiled Display Wall
Location:
NCSA booth
Investigators:
Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers:
James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG),
Avneesh Pant (NCSA)
Presenter:
Michelle Gower, NCSA
Contacts:
Michelle Gower, Avneesh Pant, and Rob Pennington at NCSA
TBG Equipment:
none
TBG Support:
Provide simulation and visualization configuration; train Michelle.
VMD already ported to display wall, NAMD binaries provided by Avneesh.
What will be demonstrated:
A NAMD simulation will be running on the NCSA Itanium Linux
cluster at SC2001
VMD will be demonstrated on NCSA's tiled display wall
powered by a cluster of low-cost graphics workstations
built with commodity parts. VMD will be used to visualize
an ongoing simulation being performed on the NCSA Itanium
cluster.
NAMD and VMD are developed by the Theoretical Biophysics Group at the
University of Illinois. NAMD and VMD development is supported by
the NIH National Center for Research Resources.
"How do you feel?" Biologists now have an answer that may
surprise you. Our sense of touch relies upon the fact that cells in
our fingertips can sense the pressure from a tabletop and
transmit a signal to the brain. But until recently, the molecular
mechanism for turning the stretching of a cell membrane into a
cellular signal was unknown. An important step in understanding
this process was the discovery of a protein known as a the
mechanosensitive channel of large conductance, or MscL.
Though this protein has been studied primarily in bacteria,
homologues exist in all major kingdoms of life. Researchers in
the Theoretical Biophysics Group have used molecular dynamics
simulations to study, at the atomic level, how MscL opens in
response to pressure changes. Models of MscL will give us new
insight, not only into how we feel, but also how our hearts beat
and how we keep our balance. Feel better now?
(more,
publication)
This is a simulation of a model of MscL from E. coli provided
by our collaborators S. Sukharev and R. Guy from the U. of Maryland and the
NIH, respectively. The SMD simulation is designed to test a proposed model
of MscL gating.
Theoretical Biophysics (TBG), NCSA and Intel McKinley Demo
Title:
unknown
Location:
Intel booth
Investigators:
Klaus Schulten, Robert Skeel, Laxmikant Kale
Developers:
James Phillips, John Stone, Justin Gullingsrud, Gengbin Zheng, Paul Grayson (all TBG),
Avneesh Pant (NCSA)
Presenter:
unknown personnel, Intel
Contacts:
Rob Pennington and Avneesh Pant at NCSA, Robert Fogel at Intel
TBG Equipment:
none
TBG Support:
Provide simulation and visualization configuration, explanatory text.
NAMD binaries provided by Avneesh.
What will be demonstrated:
NAMD will run on two to four McKinley processors. The live simulation
will be displayed with VMD running on a Linux PC.
NAMD and VMD are developed by the Theoretical Biophysics Group at the
University of Illinois. NAMD and VMD development is supported by
the NIH National Center for Research Resources.
Aquaporins make up an important family of proteins that allow water
to pass through cell membranes, while blocking undesired ions and
larger molecules. At least eleven different types of aquaporins can
be found in the human body, and their malfunction may be linked to
common diseases. Some of the aquaporins serve a double-purpose: they
also allow the movement of one or more other specific molecules into
and out of cells.
This is a simulation of GlpF, a typical aquaporin that also conducts
glycerol (a simple sugar), but lets almost nothing else through. A
molecule of glycerol is being pulled through the channel, allowing us
to see the path that it follows. By studying simulations of this
channel, TBG researchers are
learning where this channel gets its amazing filtering ability.