Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan?

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Tue, 14 Apr 2020 10:28:12 -0400

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 - 07:30:02 PDT