First, thanks for all answers. Thank you so much dear Adrian, Lorenzo and
Gustavo. Actually I looked my data again at 0 degree and at 360 degree
energies are equal but my chart in the range of 0-355 degree. I think the
referee confused blue line and red line in the chart because evenI did the
same mistake when I checked it. But I am happy to ask this question I
learned a lot of new things.
Thanks for all answers again.
Gustavo Seabra <gustavo.seabra.gmail.com>, 14 Nis 2020 Sal, 17:28 tarihinde
şunu yazdı:
> In a way, the referee is correct: One *should* expect the results at 0 and
> 360 degrees to be the same. But that is assuming nothing else changes, and
> after doing the scan (360) you arrive at exactly the same overall structure
> as in the beginning (0). What you are seeing there is, most likely, the
> effect of other degrees of freedom you are not controlling, and the
> molecule arrives at a different conformation at 360 than it had at 0.
>
> A couple of ideas for the top of my head now to solve this:
> - Do the transformation back and forth multiple times, until the results
> converge. Or,
> - At each point, you could run a small MD to generate alternative
> configurations of the other DoF, but at the same value for the angle you
> are controlling, then averaging the results, instead of relying on one
> single value for each point.
>
> All the best,
> --
> Gustavo Seabra
>
> -----Original Message-----
> From: Erdem Yeler <erdemyeler.gmail.com>
> Sent: Friday, April 10, 2020 7:02 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan?
>
> Hello,
> I parameterized a novel molecule and I sent it a as an article to journal
> and my article has been rejected.
> Here is my PES scan of x-y-z-t dihedral .
>
> [link for the picture: https://hizliresim.com/5CyhD0 ]
>
> [image: image.png]
>
> the referee says: "There is a strange transition at ~130° as well as a
> very large discontinuity at Φ = 0° and 360°. It is expected that
> Edihedral(0°) = Edihedral(360°); the green and yellow dotted lines in the
> plot below should be at the same level, but this does not seem to be the
> case"
>
> Actually I performed PES scan in gaussian09 and psi4 and I got the same
> results in different softwares so I thought this chart is not strange.
> Still I am not sure if referee is right or not. Before I send the article
> I saw some parameterization articles which didn't perform PES scan 0-360
> degree. Some of authors performed scan in the range of 0-60 degree or
> 0-120 exc.. degree and I didn't predict I will face a result like this.
> Should I perform single point energy for each angle instead of PES scan?
> or should I do another thing? What are your suggestions? How can I explain
> this?
> Thank you.
>
>
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Received on Tue Apr 14 2020 - 13:30:01 PDT
