VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat May 11 2024 - 11:09:14 CDT

..answer to above: yes RI and RIJCOSX exhibit errors magnitudes smaller
than the intrinsic error in MP2 or the basis set or the force field
simulation itself.
..and I will follow the ffTK Tutorial methods for best CHARMM
compatibility.

On Thu, Apr 25, 2024 at 5:17 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...and if I should use the ffTK ! MP2 6-31G* TightSCF opt in lieu of the
> faster ! RI-MP2 6-31G* TightSCF opt autoaux rijcosx towards best CHARMM
> compatibility feel free to let me know, thanks if you know:)
>
> On Thu, Apr 25, 2024 at 4:39 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> Hi Josh thank you for your kind update and an enriching crystal clear
>> explanation:).
>>
>> I will execute the default ffTK ! MP2 6-31G* TightSCF opt again and then
>> compare its CCGenFF Penalty Scores with the results of the RKS method and
>> Basis Set
>> and update you accordingly of the results (agreed that the MP2 will
>> provide greater CHARMM compatibility). Feel free to add any further
>> comments.
>>
>> Best,
>> Joel 🚀
>>
>>
>>
>> On Thu, Apr 25, 2024 at 4:23 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:
>>
>>> I don't think "but someone on the internet said it was ok!" will fly in
>>> a methods section, so this is something that you'll need to figure out and
>>> be able to defend. What I will say is as far as I know the standard
>>> practice in CHARMM is HF or MP2, which is the FFTK default. RKS is a DFT
>>> method, and while DFT is often useful, it is sometimes almost too
>>> permissive of garbage inputs. If DFT isn't bailing, but the other methods
>>> are, are you sure you have the right charge and spin multiplicities set?
>>>
>>> -Josh
>>>
>>> On 4/25/24 6:42 AM, Joel Subach wrote:
>>>
>>> ...meaning also is the RKS Method acceptable considering it is not an
>>> MP2 nor HF Method to my understanding? Thanks:)
>>>
>>> On Wed, Apr 24, 2024 at 4:00 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>> wrote:
>>>
>>>> Hello Josh thank you for your kind update:).
>>>>
>>>> I had amended the ! MP2 6-31G* TightSCF opt to ! RI-MP2 6-31G* TightSCF
>>>> opt autoaux rijcosx towards the Geometry Optimization and Charge
>>>> Optimization
>>>> which sped up the ORCA optimization results which successfully
>>>> functioned within Geom Opt and Charge Opt.
>>>>
>>>> I had then modified this same above Basis Set to the below in bold
>>>> which is thus far executing via ORCA without error(s) as-of-yet. RI-MP2
>>>> 6-31G* TightSCF opt
>>>> autoaux rijcosx, ! RI-MP2 def2-SVP/C TightSCF Opt NumFreq and ! RI-MP2
>>>> def2-TZVP def2-TZVP/C TightSCF Opt NumFreq PAL8, were generating
>>>> errors
>>>> within ORCA, these three would of supposedly generate hessian
>>>> output.out files to then be used within the ffTK Bond and Angle
>>>> Optimization.
>>>>
>>>> *! RKS PBE0 D3BJ def2-TZVP def2/J Opt Freq TightSCF RIJCOSX # (the
>>>> "def2/J" is the auxiliary coulomb fitting basis set)*
>>>>
>>>> Hopefully the above makes sense, my inquiry is if the above in bold
>>>> and the other Base Sets I used successfully in ORCA should be changed or do
>>>> these base
>>>> sets seem satisfactory to you.
>>>>
>>>> Thanks if you know:),
>>>> Joel 🚀
>>>>
>>>> On Wed, Apr 24, 2024 at 3:35 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>>>>
>>>>> Hi Joel,
>>>>>
>>>>> What basis set was successful? The rest of CHARMM36 uses HF/6-31G(d),
>>>>> and there are some other assumptions in parameterization that depend on
>>>>> this basis set. Like the multiplier by 1.16 between QM and MM energies is
>>>>> strictly empirical, and probably won't extend to other basis sets. If you
>>>>> are using some semi-empirical method, that probably won't be very
>>>>> compatible with the assumptions built into the CHARMM parameterization
>>>>> scheme, but if its still the HF method with a bigger basis set, that is
>>>>> probably fine.
>>>>>
>>>>> -Josh
>>>>>
>>>>> On 4/24/24 07:37, Joel Subach wrote:
>>>>>
>>>>> ....and the ffTK default ORCA Base Set is: ! MP2 6-31G* TightSCF opt
>>>>>
>>>>> On Wed, Apr 24, 2024 at 12:07 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
>>>>> wrote:
>>>>>
>>>>>> Hello VMD Forum,
>>>>>>
>>>>>> Towards the above topic, I have been executing the ffTK Tutorial
>>>>>> suggested QM Base Set, however, upon reaching the QM generated Hessian
>>>>>> Output the above base set has generated errors, accordingly I have instead
>>>>>> executed an ORCA Forum suggested Base Set which is so far executing
>>>>>> successfully.
>>>>>>
>>>>>> Would ffTK regardless suggest the ffTK Tutorial Base Set if
>>>>>> functioning in lieu of other Base sets since the HF/6-31G(d) level of
>>>>>> theory is to maintain the consistency with the CHARMM force field?
>>>>>>
>>>>>> Thanks if you know since if not to the above then I may go back and
>>>>>> use the ORCA Tutorial to modify each Base Set accordingly.
>>>>>>
>>>>>> Best,
>>>>>> Joel🚀
>>>>>>
>>>>>
>>>>> --
>>>>> Josh Vermaasvermaasj_at_msu.edu
>>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>>>> Michigan State Universityvermaaslab.github.io <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!HXCxUKc!ydv1Paa8DyAqa_YaWHP3rwEtzqGpWJ9L0W03Q-dUAqnQTzVQyqvDMLm76iu3CHvvN2chcAnXo79vyvedtpezU3A$>
>>>>>
>>>>>
>>> --
>>> Josh Vermaas
>>> vermaasj_at_msu.edu
>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>> Michigan State Universityvermaaslab.github.io
>>>
>>>