[gmx-users] Shell (Drude) model for polarization in GROMACS

Justin Lemkul jalemkul at vt.edu
Mon Jun 18 21:07:54 CEST 2018

On 6/18/18 3:00 PM, Eric Smoll wrote:
> Hello GROMACS users,
> I am looking over the shell (Drude) model for polarization in GROMACS.
> There isn't much information available in the manual (probably because this
> feature is rarely used).  I was hoping someone knowledgeable about
> polarizable simulations in GROMACS could help answer a few of my
> questions:
> (1) How exactly are Thole functions turned on? The 2018.1 manual does not
> specify. I am guessing they are hard-coded into all shell molecular
> dynamics simulations. Am I correct?

They're activated with a [thole_polarization] directive.

> (2) To add a shell to a topology, I suspect I must specify a shell atomtype
> (setting the particle type to "S" for shell) and list the shells in the
> atoms directives.  Using the "[ atomtypes ]" format in oplsaa.ff for a
> molecule with a res-name of "ABC", I assume the following will produce two
> shell particles with a charge of +1 and -1. Am I correct?
> [ atomtypes ]
> ; atom-type bond-type atomic-number mass charge particle-type sigma epsilon
> opls_9999 Sh 1 0 0 S 0 0
> ; I am guessing that
> [ atoms ]
> ; atom-number atom-type res-number res-name atom-name charge-grp charge
> 1 opls_9999 1 ABC Sh1 1 +1
> 2 opls_9999 1 ABC Sh2 2 -1
> ....

Looks right.

> (3) I suppose connectivity of each shell to its core is indicated with the
> "[ polarizability ]" directive. I am guessing "i" is the core atom and "j"
> is the shell particle.

It actually doesn't matter. mdrun figures it out on the fly based on 
particle type - see init_shell_flexcon in shellfc.cpp.

> (4) Since the code carries out an SCF calculation to relax the position of
> the shells at every timestep, I assume there is no need to specify shell
> masses or to thermostat the shell DOF.  Does GROMACS omit shell particles
> from thermostats?  The manual does not specify.

Yes. Massless particles are not subjected to dynamical update routines.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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