RE: Re: AMBER: Minimized structure

From: Linchen Gong <>
Date: Thu, 28 Jul 2005 14:55:05 +0800

Hello, Thomas
In your reply, you mentioned that energies should be reasonable. I wonder that what is reasonable.
When I run a simulation of a 200 residues protein in explicit water, the vdw energy is positive and is about 9000. Whereas the trajectory seems correct. Is the vdw too big or reasonable? Is there any hidden error?
Thanks a lot
best regards
Linchen Gong

Linchen Gong
basic science class
math and physics oriented
Department of physics
Tsinghua University
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Received on Thu Jul 28 2005 - 08:53:00 PDT
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