AMBER Archive (2008)

Subject: Re: AMBER: Amber 10 on the BlueGene

From: Robert Duke (
Date: Mon Jul 28 2008 - 12:17:18 CDT

I think the pmemd config stuff for pmemd 9 should work for pmemd 10 for BG/L - Ross and I both have some config info posted there; mine was for an IBM bluegene facility, Ross' was for the bluegene at SDSC. These may not be absolutely correct for your installation, but should provide you with a good starting point (this is under "Tips for running Amber 8 or 9 on various architectures").
Best Regards - Bob Duke
  ----- Original Message -----
  From: Mike Hanby
  Sent: Monday, July 28, 2008 12:15 PM
  Subject: AMBER: Amber 10 on the BlueGene

  Has anyone compiled Amber 10 (I guess pmemd to be precise) for the Blue Gene, and if so wouldn't mind sharing the config file and instructions?


  Also, I've read a thread or two about the difficulties of getting NetCDF support built into the Blue Gene binary, has anyone had any success with this? My Amber users are reluctant to use bintraj for their non Blue Gene jobs if the BGL will have to use the old format.


  Thanks for any help,



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