The subject of your email is "folding" but it sounds like you are trying
to simulate dimerization. Others here may be aware of successful examples
in the literature to give you a sense of the tractability of this problem.
I would suspect that far longer simulations are needed.
On Sun, Oct 30, 2022, 9:55 AM Jiaan Zhu via AMBER <amber.ambermd.org> wrote:
> Dear Amber users,
>
> I’m trying to simulate a self-complementary oligonucleotide (5
> -CTTATGGGCCCATAAG-3 ) by bsc1+TIP3P in 100nM NaCl, for 500ns. However, I
> didn’t observe any secondary structures in the trajectory. I’m wondering if
> there's anything wrong in my production run settings and how do I fix it.
> The md.in file is attached.
>
> Thanks a lot!
>
> Best regards,
> Jiaan
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Received on Sun Oct 30 2022 - 08:30:03 PDT
