AMBER Archive (2008)

Subject: Re: AMBER: energy problems in simulation with restraints

From: David A. Case (
Date: Mon Mar 31 2008 - 10:35:58 CDT

On Mon, Mar 31, 2008, Daniel Cappel wrote:

> If I start with a higher value of 10 kcal/mol and decrease it in steps
> of 1 kcal/mol the simulation crashes after the first change in the
> RESTRAINT_WT with "vlimit exceeded". If I insert a short minimization
> (only 50 steps) between two MD runs with different restraint weights,
> EEL changes from about -100,000 to -1,000,000 during the simulation. On
> the other hand the VDWAALS term increases. Then, this leads to a new
> "vlimit exceeded" and "SANDER BOMB" in the following MD step.

You need to figure out where the instability in your energies is coming from.
Look at the structures right before and after the big change in EEL to see
where you have close contacts. Or, use the "checkoverlap" command in ptraj
to see the same thing. Just fiddling with the restraint weights won't help
until you identify and fix the underlying problem.


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