[gmx-users] Implementing Drude Particles

Justin Lemkul jalemkul at vt.edu
Fri Jun 28 19:14:24 CEST 2019

On 6/27/19 10:39 AM, Finnigan, Sophie wrote:
> Dear All,
> I am relatively new to using GROMACS and MD simulations in general and I am looking to implement a polarisable FF based on the Drude oscillator model in GROMACS. There seems to be little information around though on running such simulations. Is there anywhere someone can point me to which runs an example simulation with a polarisable FF or has more information on the set up of the systems?
> I understand from the 2015 paper on the implementation of the extended Lagrangian Dynamics that it is possible to implement the Drude oscillator model, but I can’t find much information in terms of the inputs necessary in the mdp file for the simulation.
> Specific questions on this if there is nowhere in general to point me:
> - Are Drude particles still only available when using the SCF scheme or md-vv integration algorithm?
> - Is the ‘Drude’ keyword in the .mdp file recognised by the recent gromacs releases? (Doesn’t seem to be in the reference manual)
> - What other options should I be aware of (e.g. restraints etc.)

These options are not supported in any released version because the code 
is still under active development. You can get the compatible version by 
checking out the 'drude' branch of the GROMACS git repository. The input 
files given in our SI will work, with the exception that the 
'drude-rhyp' option is now called 'drude-r'. Domain decomposition does 
not work, nor does NBTHOLE, so if your system has ions, you need to use 



Justin A. Lemkul, Ph.D.
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