[gmx-users] Shell (Drude) model for polarization in GROMACS
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
> (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
> (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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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