VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Tue Feb 20 2024 - 06:06:29 CST

Hello RG Community in the above instance subsequent to the ffTK first tab
blanks will be drawn for psf, par etc., accordingly working through all
tabs depending will function best:).

On Thu, Oct 26, 2023 at 6:09 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...and I had skipped all tabs proceeding to scan torsion since I only had
> two dihedrals to optimize (maybe skipping Opt Charges tab etc.
> is causing this problem)?
>
> On Thu, Oct 26, 2023 at 10:26 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> * the MMEi and orig in red and BLUE respectively (from last original
>> message):
>>
>> ...and also my respective output.out files generated via ORCA seem to be
>> correct since the19 torsional potential conformations (in this case)
>> completed exhibiting 19 steps exhibiting visually the original file 1-step
>> after the relaxed surface scan via ORCA comparing it to the final
>> output.out file´s 19th-step, ultimately exhibiting the dihedrals 19-new
>> torsional potential conformational coordinates, this visual seems to be
>> exhibiting the correct QM ORCA generation of its output.out files (see one
>> of them via screenshot attached).
>>
>> On Tue, Oct 24, 2023 at 7:41 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>> wrote:
>>
>>> Hello VMD Community:),
>>>
>>> Towards the above topic,
>>>
>>> I had ORCA performed a relaxed surface scan for each of two dihedrals
>>> to be parameterized, however, subsequent to using my four output.out
>>> files as QM Target Data within ffTK Opt Torsions Tab, my Visualized Results
>>> Conformation to Energy respective X-Y Graph exhibits a repeated abrupt
>>> shift in the QM data (e.g. from Conf. 17 to 18) that suggests a
>>> hysteresis problem in the QM calculation, moreover my Dihedrals exhibit
>>> 4 equivalent minima which seems like a mistake (see attachment exhibiting
>>> the Black Line QME Data, the MMEi and orig in red and black
>>> respectively are the ffTK results when all dihedrals are excluded and
>>> the results of the initial optimization).
>>>
>>> If this QM Data is correct and there is another solution, such as,
>>> inputting specific phase shift and periodicity values feel free to update
>>> me accordingly, i.e. maybe the generated large RMSE is because of the input
>>> phase and multiplicity values and not the QM ORCA Results.
>>>
>>> I may perform a common test for hysteresis by running the same dihedral
>>> scan calculation backwards, i.e. reverse the sign of the rotation
>>> increment, if you may have any other suggestions feel free to reply?
>>>
>>> Thanks:)
>>> Joel [image: 🚀]
>>>
>>