VMD-L Mailing List

From: Akash Banerjee (akashneon_at_gmail.com)
Date: Tue Feb 02 2021 - 08:20:56 CST

Thank you so much for pointing this out. Yes, my dihedral does not rotate
smoothly. I will revisit my initial geometry and remove clashing groups.

Thank you for your help.

Kind regards,
Akash

On Mon, Feb 1, 2021 at 7:45 PM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:

> 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). I only scan the one that is associated with a high penalty
>>>> factor (assigned by CGenFF). I followed the routine given in the tutorial,
>>>> i.e generated a QM input file for a negative (-180 to 0) and a positive (0
>>>> to 180) scan. I kept an interval of 5 degrees for both scans for better
>>>> results.
>>>> 3. The QM simulations were run on a remote resource, and QM log files
>>>> were successfully generated.
>>>> 3. In the optimize dihedrals tab, I uploaded the modified PDB , PSF,
>>>> PAR and 2 QM target log files. I selected the dihedral that requires
>>>> optimization, and I clicked the "run optimization" button. The resultant
>>>> RMSD is 3.54.
>>>> 4. I do refinements by adding dihedrals with different periodicity and
>>>> phase shift angles. I referred to table 19 in this link:
>>>> https://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield.pdf
>>>> <https://urldefense.com/v3/__https://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.ks.uiuc.edu*2FTraining*2FTutorials*2Fscience*2Fforcefield-tutorial*2Fforcefield.pdf&data=04*7C01*7Cgumbart*40physics.gatech.edu*7C1fcaa9cfec7448969c2808d8c3e11e5f*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637474718940642800*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=cuzbs3vIOUSGSS3uZ*2BV*2BPJPHpZhrEmRT57cs9FshN*2F0*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!ulm7u_TLt0cJwwNON_1UNu7kqzzOu3YjJsKdBgHDcLfm2I1Y5iy3F4JF8-akBEoF8w$>
>>>>
>>>> After trying several combinations (i.e all possible periodicity, phase
>>>> shift angles, optimization algorithms and tolerance values), I get a RMSD
>>>> of 2.2. I am not able to reduce the RMSD beyond the 2.2 mark.
>>>>
>>>> Do you have any insights into how I could get lower RMSD values, in
>>>> turn improving the dihedral fitting protocol?
>>>>
>>>> Thank you.
>>>>
>>>> Kind Regards,
>>>> Akash
>>>>
>>>>
>>>>
>>>
>>> --
>>> akash
>>>
>>>
>>>
>>
>> --
>> akash
>>
> 

-- 
akash