VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Jun 10 2020 - 06:44:05 CDT

Please keep vmd-l in your replies.

The COLP is described in the source paper - I recommend reading it thoroughly: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874408/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874408/>

Best,
JC

> On Jun 10, 2020, at 7:38 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz> wrote:
>
> Is this via COLP? I was wondering if there was some kind of guide or manual for interpreting that. I'm unsure about what 'delta or obj' means or what to look for in terms of convergence. And why most distance plots are blank.
>
>
> Daniel Fellner BSc(Hons)
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>
>
> On Wed, 10 Jun 2020 at 23:19, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> FFTK tracks the agreement between the energies in QM and MM as well as the distances. You can identify problematic ones and try to adjust the weighting, for example, to put more emphasis on them during the fitting.
>
> I think it’s okay to help the optimization by giving it a limited range to explore, as long as the results are good.
>
> Best,
> JC
>
>> On Jun 10, 2020, at 6:56 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz <mailto:dfel694_at_aucklanduni.ac.nz>> wrote:
>>
>> I've excluded the water interactions which didn't find a minimum or were affected by secondary interactions (2x symmetrical ACC-carbonyl carbon, 2x symmetrical ACC-120 degree carbonyl, and 2x symmetrical DON-carbonyl carbon) though most of the waters found a reasonable minimum.
>>
>> "Are the interaction energies for the optimized charges in good agreement between QM and MM?"
>>
>> By this, do you mean do the QM water interaction energies (derived from delta water-complex energy v.s. molecule in vacuo HF energy) correlate with the distances? Or that the optimised charges in FFTK correlate with the HF charges? Because I haven't checked the former and the latter is where I'm seeing the problem. If I change the initial charges from the CGenFF charges to the MK dipole charges from the MP2 SP calculation, and set a range of +/-0.2 from the HF MK Dipole charges, I get more reasonable results, but I fear this may be overfitting.
>>
>> Thank you.
>>
>>
>> Daniel Fellner BSc(Hons)
>> PhD Candidate
>> School of Chemical Sciences
>> University of Auckland
>> Ph +64211605326
>>
>>
>> On Wed, 10 Jun 2020 at 05:33, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
>> FFTK is not using Mulliken charges. It’s trying to optimize the interaction energy with water molecules. As much as we might wish otherwise, FFTK can’t be treated as a black box. Look at the QM output - are all water molecules finding a minimum at a reasonable distance? Are the interaction energies for the optimized charges in good agreement between QM and MM? etc.
>>
>> Best,
>> JC
>>
>>> On Jun 9, 2020, at 12:15 AM, Daniel Fellner <dfel694_at_aucklanduni.ac.nz <mailto:dfel694_at_aucklanduni.ac.nz>> wrote:
>>>
>>> Hi all,
>>>
>>> I'm having some difficulty deriving appropriate partial charges. The charges don't seem to match chemical intuition and differ significantly from the CGenFF-assigned charges (when not specifically excluded) for even low penalty atom types.
>>>
>>> Upon reading the Gaussian output files, I actually only find Mulliken charges in the output. I was under the impression that Mulliken charges are not suitable for such uses. Is the Gaussian input script writer perhaps not providing the correct keywords for my version of Gaussian (09-D.01)?
>>>
>>> As an example, the input line for the MP2 calculation reads:
>>>
>>> # MP2/6-31G* SCF=Tight Density=Current
>>>
>>>
>>> Daniel Fellner BSc(Hons)
>>> PhD Candidate
>>> School of Chemical Sciences
>>> University of Auckland
>>> Ph +64211605326
>>
>