Gromacs and Amber on Infiniband (Biowulf)

Gromacs has been updated to v.3.3.3, and Amber to v. 10.
In addition, both packages have been built for Infiniband,
where they scale much better than on the gige nodes.

Based on our benchmarks, it is reasonable to run a 16 or 24
processor Gromacs job, or a 8-processor Amber job on the
Infiniband nodes.

Note that Amber 10 has been built with the Pathscale compilers,
so any batch scripts that were using Amber 9 (built with the
PGI compilers) will need to set a different path. Details are on
the Biowulf Amber webpage at
http://biowulf.nih.gov/apps/amber/

Details about Gromacs are at
http://biowulf.nih.gov/apps/gromacs/