Dear Ilyas and Dear Hector,
thank you so much for your answers. All answers here are very valuable and
I took them as note.
All the best,
Erdem
Erdem Yeler <erdemyeler.gmail.com>, 14 Nis 2020 Sal, 23:01 tarihinde şunu
yazdı:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Apr 15 2020 - 14:00:02 PDT
