Recent News about Amber and AmberTools

NVIDIA Announces MD SimCluster - GPU Accelerated AMBER Preinstalled (14 Sep 11)

From Ross Walker:

NVIDIA have just announced the MD SimCluster Program. A collaboration between AMBER developer Ross Walker and NVIDIA engineers to design a GPU accelerated mini cluster optimized specifically for running GPU accelerated AMBER. These machines are offered by NVIDIA's partners and come with AMBER pre-configured and ready to run.
 

GPU Computing Enabled Cluster Designed for GPU Accelerated AMBER 4 Nodes x 8 Tesla M2090 GPUs with CUDA 4.0. Dual 6-core CPUs + Infiniband QDR /node. Preconfigured With AMBER 11 (AMBER license required). No Setup necessary. Buy cluster loaded with Linux OS and cluster management software.

Try the Latest AMBER GPU Code on the Tesla MD SimCluster for Free

NVIDIA is collaborating with several system integrator partners to provide a trial program allowing people to gain remote access to the Tesla MD SimCluster, an 8 GPU computing system for free. This will allow you to see the exceptional performance offered by the latest version of GPU accelerated AMBER (GPU v2.2 [AMBER 11+ Bugfix 17]) and try it with your own simulations. All you need to do is load your models and start simulating.

Details of the MD SimCluster project along with instructions for signing up for a free trial are available by following this link or by email to mdsimcluster@nvidia.com

Additional information on recommended hardware for running AMBER on GPUs can also be found on the Main AMBER GPU webpage.

Major performance update for AMBER GPU code released (18 Aug 11)

Thanks to funding from the NSF SI2-SSE program (NSF1047875 & NSF1047919) and close collaboration with NVIDIA a major performance update is released August 18th 2011 for the GPU accelerated PMEMD package. This update, released as bugfix 17, doubles performance across the board for PME calculations while also fixing a number of outstanding bugs. A single GTX580 now runs the JAC Production NVE benchmark at over 50ns/day.

Detailed benchmarks are available on the AMBER GPU Page. The update can be obtained from the Amber 11 bugfix page.

Updated version of amberlite (21 Jun 11)

Romain Wolf has created an updated version of the amberlite package, which illustrates and automates the use AmberTools for some common tasks in amberlite_jun11.tar.gz

To install, do this:

	% cd $AMBERHOME/AmberTools
	% tar xvfz amberlite_jun11.tar.gz
	% cd amberlite
	% ./install.py

Binary version of pmemd for Windows

We are now distributing pre-built binaries for pmemd for Microsoft Windows.