VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Nov 18 2020 - 18:18:04 CST

I also recommend upgrading to the latest (alpha) version. I had an issue
with an optimisation where I had to increase the water shift to +/-2.0 to
get semi-reasonable convergence, yet using VMD 1.9.4a48 the default
settings produced an almost perfectly converged run.

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

On Thu, Nov 19, 2020 at 11:34 AM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:

> Please CC the VMD mailing list when replying.
>
> 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
>>>>
>>>>
>>>>