Hi, meng
I think the tutorial has already talked about this issue, check the section
:
The windows with negative z distance
You should define with negative distance
Best
Feng
On Mon, Aug 6, 2018 at 9:49 PM Meng Wu <wumeng.shanghaitech.edu.cn> wrote:
> Deal all,
>
> Just a quick question, could Amber16 support COM pulling in direction?
> I have read the web tutorial (
> https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial) , it's
> pulling based on distance. In my case, the small molecule that I want to
> pull is initially in the middle of the channel protein, so I divided the
> whole SMD into two parts, the up-direction part and down-direction part
> along z axis, then if I did the umbrella sampling based on distance, WHAM
> would give the wrong results. So I am wandering if it's possible to do COM
> pulling in direction, could anybody give me some suggestions? Thanks in
> advance!
>
> All the best,
> Meng Wu
>
>
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--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Aug 07 2018 - 06:00:02 PDT
