[CP2K-user] [CP2K:11464] Re: Water-bilayer/Metal interface - Ab intio MD

Anna Anic aan... at gmail.com
Thu Mar 21 19:51:47 UTC 2019

PS: I appended the corresponding output file and force.xyz
This was just a 30 min. test run to check if the parameters work

Am Do., 21. März 2019 um 20:43 Uhr schrieb Anna Anic <aan... at gmail.com>:

> Dear Marcella,
> Thank you very much for the quick response.
> To answer your questions:
> 1. Before I did the MD part I performed energy convergence test for the
> slab thickness and size, then a geometry optimization for the bulk and slab
> with and without adsorbate with a 20 Angstrom thick vacuum level
> But I just realized that the coordinates in the input file are not from
> the optimized structure. But I think that the water bilayer still should
> not behave like this
> 2. All structures converged during these calculations and surface free
> energies (SFE) are similar to reference values from other works
> 3. I did not calculate the binding energy for water molecules. Is this
> relevant if the SFE values seem to be oke?
> 4. The layers of the water molecules should represent the water structure
> in the Double Layer of an electrode/electrolyte interface. I took the
> geometry of the bilayer from a paper, that claims that the water at the
> interface is ice-like. I want to check if it stays that way (probably not)
> and sample as many water orientations (as this changes the work function)
> as possible.
> 5. Concerning the MD part I did not anneal the structure slowly. But I did
> the same calculation with a fully solvated system, so the whole vacuum
> region was filled with water, and the movement of the water molecules
> seemed reasonable.
> What temperature steps for the anneling would you suggest ?
> And do you maybe have some example input block for that?
> In general, do you think that the external potential with the parabolic
> function is oke to keep the water molecules within a certain region from
> the surface?
> Greetings,
> Anna
> Am Do., 21. März 2019 um 17:00 Uhr schrieb Marcella Iannuzzi <
> marci... at gmail.com>:
>> Dear Anna,
>> which type of calculations did you carry out in preparation of the MD run?
>> Is your DFT model reproducing the correct lattice structure?
>> Did you optimise the slab and check that the electronic structure of the
>> bulk and at the surface is what expected from reference data?
>> I do not know this specific system, but the parameters in the DFT section
>> seem to be not very well tuned. Is the SCF converging? Do you get
>> reasonable forces?
>> Did you model the adsorption of individual water molecules to evaluate
>> the binding energy and compare to references?
>> Should the layer of molecules be ice-like or do you want to simulate
>> liquid water?
>> If the coordinates are obtained from some structural data or geometry
>> optimisation, did you anneal slowly from 0K to the final temperature?
>> Why are you running NPE? Did you already thermalised at constant volume?
>> Kind regards
>> Marcella
>> On Thursday, March 21, 2019 at 3:55:19 PM UTC+1, Anna Anic wrote:
>>> Hey everybody,
>>> I am trying to do Ab-initio MD for a metal-water interface. I am using a
>>> symmetric slab and positioned a bilayer of water at both surface sites.
>>> Now, if I run the simulation my water layer just decomposes into the
>>> vacuum region. That is why I would like to implement an vacuum potential
>>> barrier at some point in the z-direction to prevent my water from just
>>> "flying away".
>>> I tried using the &EXTERNAL_POTENTIAL keyword and defined a harmonic
>>> function as a barrier.
>>> But when I run the simulation the hydrogen atoms from the H2O-bilayer
>>> are "blown away".
>>> The question is, what did I do wrong? Is the idea legit? Does anyone
>>> have a proposal how to fix the problem or how to do it differentey.
>>> Greetings,
>>> Anna
>>> (I attached my input file,geometry and trajectory )
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