[gmx-users] Steps to using Drude force field?

[Justin Lemkul]

On 8/22/19 7:48 PM, Billy Williams-Noonan wrote:
> Hey James,
>
> I was about to tell you that I don't think you can easily do this in
> GROMACS, but it turns out you might be able to with the 2019 version?
>
> Have a read
>
> http://manual.gromacs.org/documentation/2019.1/reference-manual/functions/polarization.html
>
> You would need to get the Drude parameters from somewhere though.  Unsure
> if the 2019 version of pdb2gmx will automate that.  If not, good luck
> searching for them!

While GROMACS has supported polarization for a long time, the Drude 
force field support that James refers to is not complete at not 
implemented in any released version. There are no tutorials and the 
documentation will be complete when the code is. The core features work 
but I have more work to do to clean things up and reoptimize after some 
rewriting. The code and force field are available by following:

http://mackerell.umaryland.edu/charmm_drude_ff.shtml

As I have warned many other users via this list, features like NBTHOLE 
are not supported and you should not consider this software robust 
enough for publishable research. When that is true, it will officially 
be in a GROMACS release and all aspects described in the manual. That 
unfortunately won't happen for the 2020 version, but I intend on getting 
things in good shape over the next year.

For now, use CHARMM, NAMD, or OpenMM with our Drude force field for work 
you want to publish.

-Justin

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Justin A. Lemkul, Ph.D.
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