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

[Eric Smoll]

Thanks Justin,

That is very helpful.  I can run the water example provided in your paper
with the GROMACS "drude" branch.

I have built my own tools to construct a core-shell MD topology file for my
system.  Grompp produces a tpr without complaint but mdrun crashes after
the first step with a segmentation fault and no other useful errors.  I am
trying to troubleshoot.

Is it required that each drude/shell immediately follow the atom it is
attached to in the atoms directive and the input coordinate file?  For
convenience, I have attached them to the end of each molecule?

In my topology, I manually account for the fact that drude/shell particles
are attached with bonds which count when evaluating exclusions.
Specifically, I assume a "3" in the molecules directive will take care of
all exclusions up to 3 bonds away.  To account for the extra bond lengths
introduced by drude/shell particles, I add manually add certain exclusions
for particles that should be 3 bonds away according to the atom-atom
connectivity.  Will this work or is there some "gotcha" I don't
understand.  For example, do you invalidate the moleculetype directive by
providing an exclusions directive?

Best,
Eric

On Tue, Jul 3, 2018 at 5:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/3/18 6:52 PM, Eric Smoll wrote:
>
>> Justin,
>>
>> Thanks again for the response and the guidance.  Your 2015 JCC paper on
>> the
>> subject was very helpful.
>>
>> Your code uses a different thole_polarization format.  Currently, Gromacs
>> uses the following format
>> [ thole_polarization ]
>> ;   i   j   k   l   function-number  thole-a-parameter   alpha_ij
>>  alpha_kl
>>
>> Your code seems to use
>> [ thole_polarization ]
>> ;   i   j   k   l   function-number   alpha_ij   alpha_kl
>> thole-a-parameter-1   thole-a-parameter-2
>>
>> If I would use 2.6 in the current Gromacs thole_polarization format, what
>> would I use in your thole_polarization format?
>>
>
> 1.3 for both atoms to get 1.3 + 1.3 = 2.6.  Thole's magic number quickly
> breaks down for complicated molecules, so our convention is that it is a
> per-atom value that is summed to give a new value of "a" per pair, e.g. a_i
> + a_j = a_total.
>
> -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
>
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>
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