[gmx-users] Shell (Drude) model for polarization in GROMACS
ericsmoll at gmail.com
Mon Jun 18 22:05:14 CEST 2018
Thank you so much for the rapid and clear reply! Sorry to ask for a bit
The thole_polarization isn't in the manual at all. Is it structured the
same way as the [ polarization ] directive in the manual:
[ thole_polarization ]
; Atom i j type alpha
1 2 1 0.001
If I want Thole corrections, am I correct in assuming that I should list
*all shells* in the system under this thole_polarization directive with (as
you pointed out) "i" or "j" as the shell? If "i" is the shell, "j" is the
core. If "j" is the shell, "i" is the core.
The code for "init_shell_flexcon" was very helpful. Thank you!
nstcalcenergy must be set to 1. The code says that domain decomposition
is not supported so multi-node MPI calculations are not allowed. I can
still use an MPI-enabled GROMACS executable on a single node for shell MD,
correct? Thread parallelization is still permitted, correct?
Thanks again, Justin. I hope my questions are clear and easy to answer.
On Mon, Jun 18, 2018 at 12:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> 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
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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