AMBER Archive (2005)

Subject: AMBER:

From: glc0358_at_vip.sina.com
Date: Sat Jul 09 2005 - 02:03:23 CDT

Hi all.
I'm using amber7 for md simulation. I created a GDP molecule and simulated it in explicit water. The minimization step is OK, however, when I ran md with SANDER and visualized the trajectory with vmd, I found that the system became into a mass, the bonds were stretched to terrible long.
To diagnose the reason, I tried the example of polyA-T tutorial, the same phenomena appeared. At the same time, the data in mdout file seemed stable, but was different with tutorial.
I checked the FAQ,I'm not sure whether it was the so-called blowup. Could anyone tell me why?
Thanks

Linchen Gong
department of physics
Tsinghua University
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