VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Thu Apr 25 2024 - 10:17:20 CDT

..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
>>
>>