Re: AMBER: Minimized structure

From: Carlos Simmerling <>
Date: Thu, 28 Jul 2005 06:53:45 -0400

This is known for TIP3P water. You might want to go read the original
papers on that water model, and also check the archives for more details.

Linchen Gong wrote:

>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 - 12:53:00 PDT
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