VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Aug 12 2020 - 14:25:50 CDT

Hi Yassar,

Unfortunately, I think the answer is mostly “chemical intuition” (which I largely lack - I rely on others in the lab to guide me). Long ago, Kenno Vanommeslaeghe wrote down some basic rules that are helpful:
https://mackerell.umaryland.edu/~kenno/cgenff/faq.php <https://mackerell.umaryland.edu/~kenno/cgenff/faq.php>

You can also look to other parametrization papers for examples (including some of ours). My impression from others who are much more patient than I am is that there’s a lot of trial and error combining different multiplicities to get a good fit without overfitting.

I would be happy to hear if others have better tips!

Best,
JC

> On Aug 12, 2020, at 10:34 AM, Yasser Almeida-Hernandez <yasser.almeida-hernandez_at_uni-due.de> wrote:
>
> Hi all,
>
> I am optimizing some dihedrals with penalties of my molecule. Is there any starting "rule of thumb" or something like that to modify the multiplicities for the refinement?
>
> These are the dihedrals I want to refine:
>
> CG321 CG2O5 CG321 OG301 0.7500 1 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG301 0.1800 2 180.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG301 0.0650 3 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG301 0.0300 6 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG303 0.7500 1 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG303 0.1800 2 180.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG303 0.0650 3 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> CG321 CG2O5 CG321 OG303 0.0300 6 0.00 ! from CG321 CG2O5 CG321 CG321, penalty= 45
> OG2D3 CG2O5 CG321 OG301 0.0000 2 0.00 ! from OG2D3 CG2O5 CG311 OG311, penalty= 19
> OG2D3 CG2O5 CG321 OG303 0.0000 2 0.00 ! from OG2D3 CG2O5 CG311 OG311, penalty= 19
> NG2R51 CG321 CG321 OG301 0.2000 3 0.00 ! from NG2S1 CG311 CG321 OG311, penalty= 30
> CG2O5 CG321 OG301 CG321 0.2000 3 0.00 ! from CG2O3 CG311 OG301 CG331, penalty= 16.9
> CG2O5 CG321 OG303 PG0 0.6000 1 180.00 ! from CG321 CG321 OG303 PG1, penalty= 73
> CG2O5 CG321 OG303 PG0 0.6500 2 0.00 ! from CG321 CG321 OG303 PG1, penalty= 73
> CG2O5 CG321 OG303 PG0 0.0500 3 0.00 ! from CG321 CG321 OG303 PG1, penalty= 73
>
> Since they are several, I don't know where to start.
>
> Thank you in advance.
>
> Best,
> Yasser
> --
> Dr. Yasser Almeida-Hernandez
> Postdoctoral Researcher
> Computational Biochemistry
> T03 R01 D45
> Faculty of Biology
> University of Duisburg-Essen
> Universitätsstr. 2, 45117 Essen
> Email: yasser.almeida-hernandez_at_uni-due.de
> Phone: +49 201 183 2457
>