AMBER Archive (2004)

Subject: Re: AMBER: Implicit 4r md

From: David A. Case (
Date: Fri Dec 03 2004 - 10:48:00 CST

On Thu, Dec 02, 2004, yen li wrote:

> But the total energies are still comming positive. Can
> somebody help me in finding the exact problem.

The absolute energy for a force field calculation is rarely meaningful. You
haven't said anything about the breakdown of the energies into pieces, but
it could be that the 1-4 electrostatics is positive for all reasonable
configurations. Only energy differences between conformations should be

This doesn't mean there is no problem, but there may not be.


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