Hi Feng,
Thanks for your kindly ancice! I have noticed the handling of a window with negative Z value, so I rotated the down-part windows with negative z-valus just as the web tutorial suggested. After all the windows finished running, I manually added a minus sign in front of the distance column vales for the down-part windows which originally in negative z-valus (Right or not?). When I put all the distance data files together and use WHAM to calculate the PMF, the problem appeared that the start (PMF = 0 Kcal/mol) and end points (PMF= 10 Kcal/mol) have the different values instead of a periodic curve.I think this is the "wrong" result because the substrate molecules were pulled into the water environment at both ends of the channel and the start & end points of the PMF file should be nearly zero. I personally think this is the non-periodic problem of WHAM, I have read the WHAM manual but it does not give the periodic information about distance(just angle). This is why I asked if Amber16 support COM pulling in dir
ection or not in the last email.
All the best,
Meng Wu
On Tue, 7 Aug 2018 at 8:54 AM Feng Pan <fpan3.ncsu.edu> wrote:
>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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Received on Tue Aug 07 2018 - 19:00:03 PDT
