AMBER: request for hardware recommendations

From: Parish, Carol <>
Date: Sat, 6 Oct 2007 11:59:01 -0400

Please forgive this hardware-recommendation related post. I looked
through the manual, the webpage and the reflectors and I didn't see any
recent information on this specific issue.

I would like to use AMBER for systems of about 200 residues in explicit
and implicit solvent. My budget will allow me to purchase either a
cluster of 10 dual quad core intels (80 cores) with gigE, or a much
smaller number of cores with infiniband. Should I invest in infiniband
or would gig E scale OK in the TIP3 calcs for a cluster this size? (10
boxes; 80 cores)

I have heard rumors that it can be difficult to install AMBER in
parallel on commodity clusters. Can anyone recommend linux
hardware/software combinations that work best?

Can anybody recommend a vendor who can install and test AMBER on a
gigE/intel cluster?

Can anyone recommend a good quality gigE switch? Does anyone know of a
HOWTO for configuring a switch to work optimally?

Thanks very much, Carol Parish

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 07 2007 - 06:08:00 PDT
Custom Search