VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Thu Oct 26 2023 - 11:09:03 CDT

..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: 🚀]
>>
>