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

Justin Lemkul jalemkul at vt.edu
Mon Jun 18 22:14:59 CEST 2018

On 6/18/18 4:05 PM, Eric Smoll wrote:
> Justin,
> Thank you so much for the rapid and clear reply!  Sorry to ask for a bit
> more clarification.
> 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.

You have to list everything explicitly, including the shielding factor, 
and between dipole pairs (Thole isn't between an atom and its shell, 
it's between neighboring dipoles). I honestly don't know what the format 
is; I completely re-wrote the Thole code for our Drude implementation 
(still not officially incorporated into a release due to DD issues, but 
we're close to a fix...)

> 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?

Presumably you're limited to OpenMPI, but again I have no idea about 
this code. I've never actually used it.



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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