[gmx-users] Shell (Drude) model for polarization in GROMACS
ericsmoll at gmail.com
Tue Jun 26 16:37:38 CEST 2018
In a previous thread on core/shell optimization (
"No, I've made wholesale changes to the code in the way that energies and
are computed. The current code has bugs. If you want a modified version
software, so caveat emptor), contact me off-list."
Is this still true? Is core/shell optimization broken in GROMACS 2018.1?
If so, would you mind sharing your Drude implementation?
On Mon, Jun 18, 2018 at 1:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/18/18 4:05 PM, Eric Smoll wrote:
>> 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
>> 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
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> 340 West Campus Dr.
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