VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Nov 18 2020 - 15:45:39 CST

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
>
>
>