[gmx-users] Shell (Drude) model for polarization in GROMACS
jalemkul at vt.edu
Mon Jul 9 15:28:13 CEST 2018
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
> 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:
>>> Thanks again for the response and the guidance. Your 2015 JCC paper on
>>> 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
>>> 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 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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Justin A. Lemkul, Ph.D.
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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