Re: [AMBER] Energy bumps and structure deformation while minimization of a small molecule

From: David A Case via AMBER <>
Date: Wed, 28 Jun 2023 08:20:40 -0400

On Wed, Jun 28, 2023, Kotaro TANAKA via AMBER wrote:
>I performed a 1000 step energy minimization of a small organic
>molecule, which is prepared by antechamber with GAFF2 and the
>RESP-derived charges.
>While the final configuration after minimization looks fine, but there
>were occasional huge bumps in the potential energy in the course of
>the minimization (I attached the energy plot file and the mdout file).

This is expected: almost all minimization algorithms occasionally take steps
that produce clashes and spikes in the energy. It recognizes what is
happening, and returns to conformations with low energy. It is rarely a


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Received on Wed Jun 28 2023 - 05:30:05 PDT
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