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

[Eric Smoll]

Justin,

In a previous thread on core/shell optimization (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-August/091101.html)
you state:

"No, I've made wholesale changes to the code in the way that energies and
forces
are computed.  The current code has bugs.  If you want a modified version
(beta
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?

Best,
Eric

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:
>
>> 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
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>