VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Thu Apr 25 2024 - 09:23:26 CDT

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 Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State University
> vermaaslab.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 University
vermaaslab.github.io