Re: [AMBER] Atoms overlapped in vacuum minimization

From: David A Case <>
Date: Wed, 13 May 2015 08:53:35 -0400

On Wed, May 13, 2015, Carlos Simmerling wrote:

> looking at the energy after 400 steps is difficult to evaluate, but since
> the energy is very large and negative and the vdw energy is not that high,
> I would guess that you have a parameter problem. overlapping atoms should
> give very high vdw energies. you'll need to look at your parameters and the
> antechamber output to see what's going on.

To add to Carlos' suggestions: stop the simulation after 400 steps and look at
it visually (or use the checkstructure command in cpptraj.) The most likely
culprits are hydrogen atoms that have zero vdW radii, and can get too close
to other atoms (are you using SHAKE?).


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Received on Wed May 13 2015 - 06:00:03 PDT
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