Thank you for the clarification!
Kotaro
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
>
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Received on Wed Jun 28 2023 - 06:30:02 PDT
