[AMBER] Can I did MM/GBSA analysis for a partial equilibrated system?

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 14 Jun 2010 00:00:44 +0800

Dear Sir/Madam,


A protein with two domains. I did a MD simulation for the system, but I found no matter how long I did the simulation, the RMSD did not become stable and go as high as 4 A. However, when I did the RMSD analysis without the flexible domain, it become stable in 200ps and the rest of the domains is stable for a the whole long simulation period with RMSD of 2A.


Can you share your experience with me if it is necessary to wait till all domains become stable, or can we report the movement, PCA analysis for the system to illustrate the transition or the movement of the flexible domain?


Can I did the MM/GBSA analysis even the whole system did not equilibrated yet?


Best regards,


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Received on Sun Jun 13 2010 - 09:30:03 PDT
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