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
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Received on Sun Mar 25 2007 - 06:07:48 PDT
