AMBER Archive (2007)

Subject: AMBER: anneal algorthm

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Fri Mar 23 2007 - 13:33:42 CST

Dear Amber Users,

The annealing algorithm undoubtedly affects the structure. I have noticed in
some papers they use longer annealing runs (250ps) and some use shorter ones
(50ps). Temperatures also vary between 800K and 1000K. I have noticed that the
number of NOE violations varies significantly upon the algorthm.

I know it is a vague and general question, but are there a general consensus or
guidelines that I should be following? So far I have been using annealing
schedules similar to the ones I have found in the litterature and/or the AMBER
tutorial and manual. But I have no rhyme or reason to choose one over another.

Thanks,
Seth
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu