[gmx-users] Electric double layer, how to add charge
André Farias de Moura
moura at ufscar.br
Fri Sep 18 22:21:56 CEST 2015
I use OPLSAA myself, and although it gets the wrong figures for the surface
potential and other interfacial properties, it is a known bias and you know
in which direction your results are going wrong.
IMHO, switching to other non-polarizable forcefield wouldn't work either,
since most forcefields either use quantum chemical data (from vacuum
calculations) or thermodynamic properties (from bulk solids/liquids, bulk
solutions and so on). AFAIK, there is no general forcefield out there using
either quantum chemical or thermodynamic surface properties for properly
parameterizing molecules interacting at surfaces. And even if you switch to
polarizable forcefields, they would still lack the proper parameterization
for interfacial systems, so I would stick with OPLSAA for the time being.
On Thu, Sep 17, 2015 at 8:51 AM, Andreas <adnad at gmx.net> wrote:
> thanks, very simple, changing the .top file worked perfectly.
> And I was thinking: How do I change the .gro file, will changing the .top
> be enough.
> thanks for the advice with the potential. I was thinking to calculate the
> potential (voltage) with the the poissons equation and the ion density.
> Afterwards to use the charge on my graphene layer to calculate the double
> layer capacitance (C_dl) and then maybe to show C_dl change over voltage.
> (by changing the charge, starting with a very small one. At a certain
> "voltage"(actually charge) the Cdl should stay about constant, i guess).
> Data will be used to estimate a more complex structure, sadly there is no
> direct comparison possible.
> Do you know if there are better alternatives to the OPLSAA, in Gromacs,
> for graphene edls? How to solve the problem with the potential?
> Thanks again.
> Best regards
> On Wed, Sep 16, 2015 at 23:33, André Farias de Moura wrote:
> you should edit your topology file (either top or itp) to include explicit
>> charges to each atom.
>> regarding the proper choice of charges, it depends on the surface
>> you think your system should have (mind that OPLSAA will typically produce
>> an overestimated potential as compared to experiment, if available - from
>> my experience it may be 2-3 times larger)
>> adding charges with opposite signs in different layers work as well, you
>> just need to keep track of the layer in which each atom is located and
>> edit the topology files accordingly (in this case, you'll have a neutral,
>> polar interface, as compared to the electrically charged interface
>> using only charges of the same sign)
>> On Wed, Sep 16, 2015 at 5:45 PM, Andreas <adnad at gmx.net> wrote:
>> Hello users,
>>> I want to simulate a graphene electric double layer (edl). So far i have
>>> used the cnt tutorials and the tutorial for lysozyme in water.
>>> All modification to the OPLSAA field parameter (atomname2type.n2t,
>>> atomtypes.atp, ffbonded.itp, ffnonbonded.itp) which i have done were with
>>> zero charge and i could already simulate a graphite layer in a box filled
>>> with water and ions, similar to the lysozyme tutorial.
>>> How and then to add a charge to the graphene layer, or if two graphene
>>> layers are added, how to add opposite charges to them?
>>> Or is there a more simple way to MD simulate an edl, in gromacs,
>>> I would be very thankful for any help
>>> Best regards
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
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