Hi,
You may find the following system preparation protocol useful:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
On Tue, Sep 1, 2020 at 2:32 AM <neildancer.sina.com> wrote:
> Hello, Amber users!
>
> Recently, I want to empoly Amber program packages to simulate a
> protein in water system in order to guide my wet experiments. I plan to use
> the cuda-version of Amber18 to run. But I had mentioned some tips from
> amber18 manual that was "Avoid using the NPT ensemble (ntb=2) when it is
> not required; if needed make use of the Monte Carlo barostat (barostat=2).
> Performance will generally be NVE>NVT>NPT (NVT~NPT for barostat=2)." In my
> knowledges, the protein-salt-water system was should be considered to
> simulate under the npt ensemble for final MD production. So, I'm confused
> whether to chose the option ntb=1 or ntb=2. I known that the
> protein-salt-water simualtion should be equilibrated by NVT and NPT
> ensemble before MD production. So, How should I process the simulation
> with amber18 cuda version. Please help me. Any suggestion is welcome.
>
>
>
> Best wishes!
>
>
>
> Ning Wang
>
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Received on Fri Sep 04 2020 - 11:00:03 PDT
