VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Mon Feb 01 2021 - 18:45:03 CST

Judging by your QM PES, it looks like you have contaminating secondary
interactions. Have you analysed the scan output to see if the dihedral
rotates smoothly? You may need to remove clashing groups.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Tue, Feb 2, 2021 at 6:11 AM Akash Banerjee <akashneon_at_gmail.com> wrote:

> Hello,
>
> I have attached the potential fits before and after refinement. I am
> seeing 2 peaks, and hence I tried refitting with a periodicity of 2.
> However, that does not really reduce the RMSE. When I assign 2 more
> dihedrals with a periodicity of 1, there is minor improvement in the RMSE
> (3.4->2.2). Since I am adding so many dihedrals (4 in number, please see
> attached dihedrals.png), I guess I am over fitting.
>
> More details about my system: I have a polymer backbone with aromatic side
> chain groups. I just need to use FFTK to parameterize the dihedral that
> connects the aromatic side chain to the backbone.
>
> From my side, I am thinking that these could be potential issues:
> 1. Initial geometry (fixed it with geometry optimization in FFTK itself)
> 2. How I am sampling the dihedral (just following the tutorial, i.e do a
> scan from -180 to 0, and then 0 to 180)
> 3. Sampling rate ( at intervals of 5 degrees to get good statistics)
> 4. How I upload the QM target data to FFTK (first negative scan, and then
> the positive scan)
>
> Please help me figure out what could be wrong. Since I am new to QM and
> FFTK, I could be missing some fundamental details.
>
> Thank you.
>
> Kind Regards,
> Akash
>
> On Mon, Feb 1, 2021 at 10:49 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
>> I think it should be possible to fit a single dihedral perfectly. Does
>> the potential look unusual in some way?
>>
>> Best,
>> JC
>>
>> On Jan 28, 2021, at 5:28 PM, Akash Banerjee <akashneon_at_gmail.com> wrote:
>>
>> Hi VMD Developers,
>>
>> I just wanted to follow up on the above ticket. Should I provide my input
>> files to clarify the issue? Please let me know if I could provide any
>> additional information that could help in this regard.
>>
>> Thank you.
>>
>> Kind regards,
>> Akash
>>
>> On Mon, Jan 18, 2021 at 5:31 PM Akash Banerjee <akashneon_at_gmail.com>
>> wrote:
>>
>>> Hi FFTK/VMD developers,
>>>
>>> I am trying to resolve a dihedral in a polymer chain. I have generated
>>> the QM target data, but I am facing difficulties in fitting the dihedral to
>>> the target. I have enlisted my protocol below. Please have a look and
>>> advise me on how I could correct it.
>>>
>>> 1. Generated an optimized trajectory (fit to QM data), and used the
>>> modified PDB file for further studies.
>>> 2. Scanned the dihedral of interest (my molecule has several dihedrals)--0000000000009c7e3105ba4fc8df--