AMBER Archive (2009)

Subject: [AMBER] heating advice

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Wed May 27 2009 - 15:44:26 CDT

 I was just curious to see if anyone has advice about how I should handle my protein. I have started MD simulations with it at 300 degrees, and I know it doesn't blow up, the backbone hardly changes. Is it still worthwhile to start at 0 degrees and heat the protein slowly during the MD? Is that going to yield better results still? Same story with energy minimizing only the Hydrogens first, then later all the heavy atoms? Are multiple minimization steps necessary if my system isn't blowing up?
Thanks,
Mark
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