AMBER: ibelly

From: Amber Administration <>
Date: Fri, 3 Oct 2003 11:55:02 -0700


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Date: Mon, 29 Sep 2003 09:03:05 -0700 (PDT)
From: nie beining <>
Subject: ibelly

Dear Amber users,

       I first energy minimized our system with water molecules and ions (13,591 atoms), then equilibrated water molecules and ions by fixing protein using "ibelly", and finally simulated the whole system allowing everything to move for 5 ns. At the very beginning of the simulation of 5 ns, however, I found that important residues at active site blew up at room temperature, also happened with 1 K initial temperature. They gradually formed hydrogen bonds. But formations are incorrect. I didn't pick up the velocities from
equilibration step. Why is my system unstable? Is it because of ibelly? How to avoid this blow-up? Many thanks!

  Beining Nie

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