<div dir="ltr"><div>Hi,</div><div><br></div><div>I looked at your input files and found many *inappropriate* options for the PM3 calculations, which are too many to be fully enumerated in this short reply.</div><div><br></div><div>1. %FORCE_EVAL%SUBSYS%CELL: The Diels-Alder reaction is a gas-phase chemical reaction, isn't it? The default value of PERIODIC in this section is XYZ. Please specify PERIODIC NONE explicitly.</div><div><br></div><div>2. %FORCE_EVAL%DFT%QS%SE%COULOMB and</div><div>3. %FORCE_EVAL%DFT%QS%SE%EXCHANGE are used for setting up CUTOFF in the evaluation of the semiempirical Hamiltonian, e.g. core Hamiltonian plus the two electron parts, so that some *numerically* insignificant integrals can be safely neglected in a practical calculation and hence saving the computation time. Are the values you set in your input files appropriate for your system?</div><div><br></div><div>4. %FORCE_EVAL%DFT%MGRID is completely irrelevant to any semiempirical methods. Please remove the entire section.</div><div><br></div><div>5. Your settings for EPS_SCF in both %FORCE_EVAL%DFT%SCF and %FORCE_EVAL%DFT%SCF%OUTER_SCF are completely *incompatible* with the default settings in Gaussian. If my memory serves me well, the default value for SCF convergence in Gaussian is 10^-8 au for geometry optimization and it's less for single-point energy evaluation. Please check!</div><div><br></div><div>6. Please find the other inappropriate options in the geometry optimization section in your input files...</div><div><br></div><div>Xin<br></div><div><br></div><div> <br></div><div><br></div><div><br></div>On Thursday, October 24, 2019 at 1:33:55 PM UTC+2, Salomé Llabrés wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Hi, </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">I am trying to reproduce a tutorial that uses Gaussian with CP2K, and I have problems reproducing the results originally achieved. </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">The tutorial describes a fairly simple Diels-Alder reaction using PM3 semiempirical. This is an old GROMACS tutorial that uses Gaussian98: <a href="http://wwwuser.gwdg.de/%7Eggroenh/EMBO2004/html/qmvacuum.html#top" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwwwuser.gwdg.de%2F%257Eggroenh%2FEMBO2004%2Fhtml%2Fqmvacuum.html%23top\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHlRu5nftmmWXwqXAf3Vub8hYA7qw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwwwuser.gwdg.de%2F%257Eggroenh%2FEMBO2004%2Fhtml%2Fqmvacuum.html%23top\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHlRu5nftmmWXwqXAf3Vub8hYA7qw';return true;"><span style="color:#dca10d">http://wwwuser.gwdg.de/%<wbr>7Eggroenh/EMBO2004/html/<wbr>qmvacuum.html#top</span></a> </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">I was able to reproduce the reactant, transition state and product energies described in the tutorial using Gaussian09. However, when I attempted to reproduce the results with CP2K, I do not obtain the same energy profile. </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">I am asking for advice on how to fix this problem and obtain reproducible results in CP2K. </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";color:rgb(220,161,13)"><span style="color:#000000">I have documented the protocol to run these simple calculations here : </span><a href="https://github.com/bioexcel/cp2K_qmmm_tutorials_for_biological_simulations/tree/master/GMX_DAA" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbioexcel%2Fcp2K_qmmm_tutorials_for_biological_simulations%2Ftree%2Fmaster%2FGMX_DAA\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH4DhYyenRggMdAqe6CneN4J4L4TA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbioexcel%2Fcp2K_qmmm_tutorials_for_biological_simulations%2Ftree%2Fmaster%2FGMX_DAA\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH4DhYyenRggMdAqe6CneN4J4L4TA';return true;">https://github.com/bioexcel/<wbr>cp2K_qmmm_tutorials_for_<wbr>biological_simulations/tree/<wbr>master/GMX_DAA</a></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">These are the results I obtained so far. </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<table style="border-collapse:collapse" cellspacing="0" cellpadding="0">
<tbody>
<tr>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><b>Energy / kJ mol-1</b></p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><b>Reactants</b></p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><b>Transition States</b></p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><b>Product</b></p>
</td>
</tr>
<tr>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">GMX Tutorial (Gaussian98)</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">0.00</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">202.17</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">-34.13</p>
</td>
</tr>
<tr>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Gaussian09</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">0.00</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">200.06</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">-36.37</p>
</td>
</tr>
<tr>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">CP2K</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">0.00</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">152.65</p>
</td>
<td style="border-style:solid;border-width:1.0px 1.0px 1.0px 1.0px;border-color:#9a9a9a #9a9a9a #9a9a9a #9a9a9a;padding:1.0px 5.0px 1.0px 5.0px" valign="top">
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">-175.81</p>
</td>
</tr>
</tbody>
</table>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">I tried to fine-tune the parameters of the input file but I cannot find the reason behind these different energy profiles. Here it is a list of the different attempts to solve this problem I tried: </p>
<ul>
<li style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><span style="font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo"></span>The optimiser has a very significant effect on the structure.</li>
<ul style="list-style-type:disc">
<li style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><span style="font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo"></span>CG gets a similar structure than Gaussian.</li>
<li style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><span style="font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo"></span>BFGS leads to the structure after SO2 expulsion. This method cannot be used with the DIMER method. </li>
</ul>
<li style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><span style="font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo"></span>SCF convergence: Using MAX_SCF 2000 is useful to converge the SCF in these simulations.</li>
<li style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue""><span style="font-stretch:normal;font-size:10px;line-height:normal;font-family:Menlo"></span>GRID CUTOFF convergence doesn't affect the accuracy of these small systems.</li></ul>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Please find attached input and output files for these files. Also you can find the protocol used in this GitHub environment: <a href="https://github.com/bioexcel/cp2K_qmmm_tutorials_for_biological_simulations/tree/master/GMX_DAA" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbioexcel%2Fcp2K_qmmm_tutorials_for_biological_simulations%2Ftree%2Fmaster%2FGMX_DAA\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH4DhYyenRggMdAqe6CneN4J4L4TA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fbioexcel%2Fcp2K_qmmm_tutorials_for_biological_simulations%2Ftree%2Fmaster%2FGMX_DAA\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH4DhYyenRggMdAqe6CneN4J4L4TA';return true;">https://github.<wbr>com/bioexcel/cp2K_qmmm_<wbr>tutorials_for_biological_<wbr>simulations/tree/master/GMX_<wbr>DAA</a></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Thank you very much in advance, </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue";min-height:14px"><br></p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Salomé Llabrés, PhD </p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">Applications developer in Data science</p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">EPCC</p>
<p style="font-stretch:normal;font-size:12px;line-height:normal;font-family:"Helvetica Neue"">University of Edinburgh, UK</p></div></blockquote></div>