<div dir="ltr">PS: I appended the corresponding output file and <a href="http://force.xyz">force.xyz</a><div>This was just a 30 min. test run to check if the parameters work<br><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Am Do., 21. März 2019 um 20:43 Uhr schrieb Anna Anic <<a href="mailto:aan...@gmail.com">aan...@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear Marcella,<div><br></div><div>Thank you very much for the quick response. </div><div>To answer your questions:</div><div>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</div><div><br></div><div>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</div><div><br></div><div>2. All structures converged during these calculations and surface free energies (SFE) are similar to reference values from other works</div><div>3. I did not calculate the binding energy for water molecules. Is this relevant if the SFE values seem to be oke?</div><div>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.</div><div>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. </div><div>What temperature steps for the anneling would you suggest ?</div><div>And do you maybe have some example input block for that?</div><div><br></div><div>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?</div><div><br></div><div><br></div><div><br></div><div>Greetings,</div><div>Anna</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Am Do., 21. März 2019 um 17:00 Uhr schrieb Marcella Iannuzzi <<a href="mailto:marci...@gmail.com" target="_blank">marci...@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><br></div>Dear Anna, <div><br></div><div><br></div><div>which type of calculations did you carry out in preparation of the MD run?</div><div>Is your DFT model reproducing the correct lattice structure?<br></div><div>Did you optimise the slab and check that the electronic structure of the bulk and at the surface is what expected from reference data?</div><div>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?<br></div><div><br></div><div>Did you model the adsorption of individual water molecules to evaluate the binding energy and compare to references? </div><div>Should the layer of molecules be ice-like or do you want to simulate liquid water?</div><div>If the coordinates are obtained from some structural data or geometry optimisation, did you anneal slowly from 0K to the final temperature?</div><div>Why are you running NPE? Did you already thermalised at constant volume?</div><div><br></div><div>Kind regards</div><div>Marcella</div><div><br></div><div><br></div><div><br><br>On Thursday, March 21, 2019 at 3:55:19 PM UTC+1, Anna Anic wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hey everybody,<div><br></div><div>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. </div><div>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".</div><div>I tried using the &EXTERNAL_POTENTIAL keyword and defined a harmonic function as a barrier.</div><div>But when I run the simulation the hydrogen atoms from the H2O-bilayer are "blown away".</div><div>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.</div><div><br></div><div>Greetings,</div><div><br></div><div>Anna</div><div><br></div><div>(I attached my input file,geometry and trajectory )</div></div></blockquote></div></div>
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