That seems unusual. Can you share your leap input? That's also where
important things are set.
On Sun, Jan 22, 2023, 6:40 AM Jiaan Zhu via AMBER <amber.ambermd.org> wrote:
> Dear Amber users,
>
> I’m trying to run simulations for a 8-mer ssDNA with artificial
> nucleotides by GBn2 model. I ran 5000 steps of energy minimization and then
> equilibration. I encountered phosphate aggregation in the equilibration
> step, as shown in the attached image. I checked the terms in the output
> file and found the rms fluctuation of EELEC and EGB were very large, EELEC
> significantly increased and EGB significantly decreased. I’m wondering if
> someone ever met a similar problem and how to deal with it. For normal
> ssDNA(without artificial nucleotides) everything works well, it only
> happens when adding new nucleotides.
>
> My prmtop/prmcrd files, min.in, equ.in files are attached.
>
> Best regards,
> Jiaan
>
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Received on Sun Jan 22 2023 - 06:00:02 PST
