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

From: Kotaro TANAKA via AMBER <>
Date: Wed, 28 Jun 2023 22:04:03 +0900

Thank you for the clarification!


On 2023/06/28 21:20, David A Case wrote:
> 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
> problem.
> ....dac

AMBER mailing list
Received on Wed Jun 28 2023 - 06:30:02 PDT
Custom Search