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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