AMBER Archive (2004)

Subject: Re: AMBER: Deeper problem with the energetics of the system

From: David A. Case (
Date: Fri Jun 18 2004 - 13:20:20 CDT

On Fri, Jun 18, 2004, nlxc wrote:

> -- restrain
> 5000.0

Try reducing the above by about three orders of magnitude (e.g. to 5-10).

> But I always got the following error after even the first round of MD
> vlimit exceeded for step 2; vmax = 36.0015791

> If I removed the restrain to allow all atoms to move, the MD is able to run
> without any problem. But I can't afford to run MD for the whole protein.

The calculation is no cheaper with the restraints or without them.


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