From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Thu Jun 25 2009 - 00:08:29 CDT
Hi,
I'm running a somewhat big monomer protein with about 448 residues and about 7000 atoms, the total number after adding periodic water box is 80383. It gets 11 beta-sheet and 13 alpha-helices.At the beginning 5 ns, everything goes well. While after 5 ns, its total secondary structure number, let's ignore what happens to tertiary structure firstly, start decreases, especially those alpha-helices who contact with water moleculars. Till 15ns, there are only 6 alpha-helices left and 10 beta-sheets. As to the tertiary structure, the whole struture seems to unstable after 15ns.
The protein's intrinsic allosteric trait require a long-time running.
Whit such a problem, i'm not be able to go on with my simulation.
What should i do ?
Can anybody help me out?
Thanks so much for your kind consideration and look forward to your reply!
Good day!
Yandong,
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