<div dir="ltr"><div><div><div><div><div>Dear Maxime,<br><br>>>So I'll conclude that this behaviour is a shortcoming of <br>>>the Siepmann-Sprik potential (at least in the current,<br>>>canonical parametrization). As I'm not really comfortable<br>>>with such a discrepancy between the QM/MM and full-QM<br>>>results, I think I will be trying to amend the potential.<br><br></div>In the Siepmann-Sprik potential there is a term that depends on the orientation of the dipole vector of the water molecule; Equation (1) and Equation(3) in <a href="https://doi.org/10.1063/1.469429" target="_blank">https://doi.org/10.1063/1.4694<wbr>29</a> The purpose of this term is to direct the hydrogens away from the surface.<br></div>If you want to change the behavior of the potential, then you have to modify this term. But as I said, during MD runs it is a rare event that the hydrogen point toward the surface. <br><br>>>Could you further clarify why the cell size would be too <br>>>small for IC-QM/MM calculations? Do you mean too small <br>>>to be relevant to real interfaces? Then I agree, but this is <br>>>just a test, and I would expect these short Pt-H distances<br>>>to also occur in larger cells (as you found yourself) --<br>>>if I replicate the structure in the X and Y directions, for<br>>>example, I assume I would be getting the same result.<br>>>Or do you mean something else?<br><br></div>Well, if you just want to see if the code runs through it's fine. For anything else (e.g. testing of bonding distances) I would not trust the results. But yes, these short distances can occur for "H-down" water molecules. However, these "H-down" structures have been also observed by full DFT calculations and experiments, see <a href="https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.89.276102">https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.89.276102</a>.<br><br></div>Best regards,<br></div>Dorothea<br> </div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-19 12:43 GMT+02:00 Maxime Van den Bossche <span dir="ltr"><<a href="mailto:maxime.cp.v...@gmail.com" target="_blank">maxime.cp.v...@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Dorothea,<br><br>Thanks a lot for attending this issue (and for your efforts in<br>developing and implementing this method)! I hadn't noticed <br>that the figure in your paper was also showing the presence <br>of such short Pt-H distances.<br><br>So I'll conclude that this behaviour is a shortcoming of <br>the Siepmann-Sprik potential (at least in the current,<br>canonical parametrization). As I'm not really comfortable<br>with such a discrepancy between the QM/MM and full-QM<br>results, I think I will be trying to amend the potential.<br><br>Could you further clarify why the cell size would be too <br>small for IC-QM/MM calculations? Do you mean too small <br>to be relevant to real interfaces? Then I agree, but this is <br>just a test, and I would expect these short Pt-H distances<br>to also occur in larger cells (as you found yourself) --<br>if I replicate the structure in the X and Y directions, for<br>example, I assume I would be getting the same result.<br>Or do you mean something else?<br><br>Best,<br>Maxime<div><div class="h5"><br><br><br>On Thursday, January 18, 2018 at 7:13:52 PM UTC, Dorothea Golze wrote:</div></div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><div><div><div><div><div><div><div><div><div><div><div>Hi Maxime,<br><br></div>there is most likely nothing wrong with the force field implementation etc. I ran quite a few simulations with the Siepmann-Sprik forcefield + image charge setup and did not encounter any problems so far.<br>Some explanations:<br></div>The Pt-O distance is approximately 2.4 Angstrom with the Siepmann-Sprik force field (see <a href="https://doi.org/10.1063/1.469429" rel="nofollow" target="_blank">https://doi.org/10.1063/1.4694<wbr>29</a> Tab. 1). In most cases, the O-H bonds are roughly parallel to the surface or point away from it. However, in some cases the H atoms point towards the surface, and in this case the Pt-H bond is only 1.5 Angstrom. This is demonstrated in Figure 11 (d) in <a href="https://doi.org/10.1021/ct400698y" rel="nofollow" target="_blank">https://doi.org/10.1021/ct4006<wbr>98y</a> .The onset of the red curve is already at 1.5 Angstrom (but the peak is at 2.4 Angstrom, so most Pt-H distances are 2.4 Angstrom).<br></div>Another important point, your "super-cell" is only 3x4 gold atoms. That's way too small. Might be that you also see some more funny effects due to this.<br><br></div>Your points above<br><br></div>>a) ... something is wrong in my input? I also got the <br> same results with narrower Gaussians for the image <br></div> charge distributions (5 Å^-2 instead of 3.5 Å^-2).<br><br></div>No, it is also correct that you see the same results with different IC Gaussian widths (that's good) . Keep the default.<br><br></div>>b) ... this is related to the Siepmann-Sprik potential <br> parameters? I couldn't find previous works, though, <br> (such as this forum, the original paper, or the<br> implementation paper) reporting such behaviour.<br> But if this is the cause, I could just add a short-<br> ranged repulsive potential to the Pt-H interaction<br> or maybe modify the Phi function in Eq 3 of the <br> original paper. Could it be that one really needs <br> to reparametrize the potential because of the <br></div> differences between DFT-water and SPC/E-water?<br></div>Of course you can always reparametrize if you wish, however, I think there is not actually a problem, see above.<br></div><div><br></div><div>>c) ... this is related to the implementation of the <br> Siepmann-Sprik potential and/or image charges<br> in CP2K?<br>>d) ... something else?</div><div><div><div><div><div><div><div><div><div><div><div>see above</div><div><br></div><div><br></div><div>Best regards, <br></div><div>Dorothea<br></div></div></div></div></div></div></div></div></div></div></div></div></div></div><div><br><div class="gmail_quote"><div><div class="h5">2018-01-18 16:30 GMT+02:00 Maxime Van den Bossche <span dir="ltr"><<a rel="nofollow">maxime....@gmail.com</a>></span>:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Dear all,<br><br>I've been interested in applying the IC-QM/MM approach<br>implemented in CP2K to investigate certain metal-water<br>interfaces. I would like to describe the water with DFT,<br>the metal using some forcefield, and the metal-water <br>interactions via the Siepmann-Sprik potential plus image <br>charge electrostatics.<br><br>During my initial testing of H2O layers on a Pt(111)-c(3x4)<br>substrate, I found some of the structures (with the <br>bottom H2O molecules adsorbed H-down) to display overly <br>short Pt-H bond lengths (1.6 Å). I've attached the <br>coordinates of such a structure, and the input with <br>which this (relaxed) structure was obtained. For simplicity /<br>familiarity, the input file is essentially identical to<br>that of the online Pt(111)-H2O how-to example.<br><br>The output (with CP2K version 6.0, commit 8b033c3) <br>is also attached. As can be seen from the 'run-r-1.out' <br>file, the Pt atoms underneath the down-pointing H atoms <br>acquire a negative image charge of around -0.07 a.u., <br>which still seems to be reasonable.<br><br>When running a full DFT (PBE-D3) optimization of the same <br>structure, the Pt-H bond lengths expand to more believable <br>values of around 2.15 Å.<br><br>So, I'm wondering what is going on, because there seem<br>to be different possibilities. Do you think ...<br><br>a) ... something is wrong in my input? I also got the <br> same results with narrower Gaussians for the image <br> charge distributions (5 Å^-2 instead of 3.5 Å^-2).<br><br>b) ... this is related to the Siepmann-Sprik potential <br> parameters? I couldn't find previous works, though, <br> (such as this forum, the original paper, or the<br> implementation paper) reporting such behaviour.<br> But if this is the cause, I could just add a short-<br> ranged repulsive potential to the Pt-H interaction<br> or maybe modify the Phi function in Eq 3 of the <br> original paper. Could it be that one really needs <br> to reparametrize the potential because of the <br> differences between DFT-water and SPC/E-water?<br><br>c) ... this is related to the implementation of the <br> Siepmann-Sprik potential and/or image charges<br> in CP2K?<br><br>d) ... something else?<br><br><br>The online how-to:<br><a href="https://www.cp2k.org/howto:ic-qmmm" rel="nofollow" target="_blank">https://www.cp2k.org/howto:ic-<wbr>qmmm</a><br><br>The original Siepmann-Sprik paper:<br><a href="https://doi.org/10.1063/1.469429" rel="nofollow" target="_blank">https://doi.org/10.1063/1.4694<wbr>29</a><br><br>The IC-QM/MM implementation paper:<br><a href="https://doi.org/10.1021/ct400698y" rel="nofollow" target="_blank">https://doi.org/10.1021/ct4006<wbr>98y</a><br><br>Best,<br>Maxime<span><font color="#888888"><br></font></span></div></div></div><span><font color="#888888"><div><div class="h5">
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