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

[Justin Lemkul]

On 7/9/18 1:31 AM, Eric Smoll wrote:
> 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?

There is no such requirement (you'll note that the water Drude is at the 
end of the atom listing in SWM4-NDP, to avoid changes in the SETTLE code).

> 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?

Sounds right, but without an actual example, I can't tell you anything 
really useful.

-Justin

>
> 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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-- 
==================================================

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

==================================================