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From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Nov 18 2020 - 16:34:30 CST

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The distances will vary as much as you let them (with the water shift
settings) to achieve the best fit. The energies are more important.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Thu, Nov 19, 2020 at 11:16 AM Lokendra Poudel <poudel_2039_at_tamu.edu>
wrote:

> Hi Daniel,
>
> I checked the energy and distance of individual atoms. The energies look
> ok but distances have highly fluctuated. Do have any thought about this?
> Moreover, the total energy and dipole seem fine but not distant.
>
> Thanks
> Lokendra Poudel, PhD
>
> On Wed, Nov 18, 2020 at 3:45 PM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
> wrote:
>
>> You'll probably rarely get convergence as good as the tutorials.
>>
>> A few things:
>>
>> 1. You probably don't need to optimise charges with low penalty scores
>> (<10 ~ 20). If you're still having issues with validation and you've tried
>> everything else, that's when I'd go back and reoptimise these low penalty
>> charges
>> 2. Check the output after your runs and you can find out which
>> interactions are causing the problem (large QME-MME deviation) and weight
>> them lower accordingly. This will improve your fit. Also, ensure there are
>> at least as many interactions loaded as there are atoms you're trying to
>> optimise.
>> 3. You're probably closer to a good solution at the higher water shift
>> settings. I'm not sure why this is, but it should be reflected in the
>> objective function.
>>
>>
>> *Daniel Fellner BSc(Hons)*
>> PhD Candidate
>> School of Chemical Sciences
>> University of Auckland
>> Ph +64211605326
>>
>>
>> On Thu, Nov 19, 2020 at 9:37 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
>> wrote:
>>
>>> Hi Lokendra,
>>>
>>> I think we usually run SA first and then downhill. But it’s quite
>>> possible there is no unique solution. Instead, you likely have a very
>>> rugged energy landscape sprinkled with local minima that you are hopping
>>> between. This is going to be compounded if you have too many charges to
>>> optimize at once. So you’ll just have to decide what interactions are most
>>> important to get right (use COLP to help).
>>>
>>> Best,
>>> JC
>>>
>>> On Nov 18, 2020, at 11:12 AM, Lokendra Poudel <poudel_2039_at_tamu.edu>
>>> wrote:
>>>
>>> Hi James,
>>>
>>> I am trying to develop parameter and topology files for a hydrophobic
>>> ligand PDBu (76 atoms) using Force Field Toolkit (FFTK). I am in charge
>>> optimization step in fftk. The quantum mechanical calculations for
>>> water interaction sites run fine. After this, I tried to optimize
>>> the charge but the optimized charges are not converged .i.e charges are
>>> changing each iteration during optimization.
>>> During optimization, I did the following steps
>>> 1/ in charge constraints: removed all non-polar Hydrogen and those
>>> atoms which have zero penalty score (CGENFF Program)
>>> 2/ in QM Target data: excluded those QM water interactions
>>> which clashing with other atoms and fly away from an atom.
>>> 3/ in advance setting: used simulated annealing with a different
>>> combinations such as
>>> water shift setting +/-0.4, +/- 1.0, +/- 1.5, +/-2.0 and delta 0.05 or
>>> 0.1
>>> optimize setting tolerance 0.005 0.001 0.01 distance weight 0.5/1.0 etc
>>>
>>> After several attempts, my optimized charges are not converged. I spent
>>> almost more than two weeks on this but couldn't fix the problem. I
>>> would appreciate it if you could help me with it.
>>>
>>> Thanks
>>> Lokendra Poudel, PhD
>>>
>>>
>>>