Hi, Meng
It is hard to say where the problem is, I would suggest you to check the
trajectories of results to see if the umbrella
sampling at each window is good.
Best
Feng
On Sun, Jul 29, 2018 at 9:52 PM Meng Wu <wumeng.shanghaitech.edu.cn> wrote:
> Since maybe my last e-mail has been ignored, forgive me send it again.
> Could anybody give me some suggestions?
>
> Best regards,
> Meng Wu
> ________________________________________
> 发件人: Meng Wu
> 发送时间: 2018年7月28日 22:26
> 收件人: amber.ambermd.org
> 主题: Inquries about Non-periodic PMF profile
>
> Dear all,
>
> I was using WHAM to analyze the PMF profile for a channel
> transportation. However, the start (PMF = 0 Kcal/mol) and end points(PMF=
> 10 Kcal/mol) have different values instead of a periodic curve. I did the
> umbrella sampling with amber16 and refered the
> "AMBER-Umbrella_COM_restraint_tutorial"(
> https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial), and
> my WHAM command is: wham -25 25 8600 0.00000001 310 0 actdata.dat out.pmf.
> I firstly did the SMD to pull the substrate molecule which initially stays
> in the middle of the channel in up and down along the z direction
> separately, then 86 windows in total were extracted to do the restraint
> simulations.
>
> Could anybody give me some advice about this problem? Thank you 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 Mon Jul 30 2018 - 12:30:02 PDT
