|
|
|
|
|
|
|
NAMD is a parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.
NAMD scales
to hundreds of processors on high-end parallel platforms and
tens of processors on commodity
clusters
using switched fast ethernet.
NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and
is distributed free of charge with source code.
You can build NAMD yourself or download
binaries
for a wide variety of platforms.
|
| Spotlight: More Commodity Supercomputing (Jul 2001) |
|
Our low-cost cluster of 32 Athlon PCs (see
February 2001 highlight)
has been in constant use by local users, providing a substantial and
very cost-effective boost to the Resource's large-scale simulation
capabilities.
To satisfy demand, we have added two additional 32-processor
clusters with
higher performance at an even lower cost.
On this platform, the freely available simulation code
NAMD can complete a 1 nanosecond simulation
of the 60,000 atom
aquaporin-1 water
channel with full electrostatics and constant pressure in a single week.
We have given two tutorials,
both filled to capacity, introducing participants to cluster hardware and
software with the aid of a hands-on session assembling and installing
four-processor clusters (see photo).
A third tutorial is scheduled for Friday, July 13.
|
image size:
41.0KB
|
|
|
|
