<div dir="ltr">Hi Jadzia,<div><br></div><div>I don't major in physical or chemistry, so what you have suggested confused me for a long time. My example comes from the following page: <a href="https://www.google.com/url?q=https%3A%2F%2Fwww.cp2k.org%2Fexercises%3A2017_ethz_mmm%3Aqmmm&sa=D&sntz=1&usg=AFQjCNGiF0gJ6mRlaGSe7--tVuWgLftgjA" target="_blank" rel="nofollow" style="cursor: pointer;">https://www.cp2k.org/<wbr>exercises:2017_ethz_mmm:qmmm</a>. </div><div><br></div><div>The simulation uses the same molecular model (as far as I know, it's true) for the MM region (I use the same potential function through 1-layer simulation and 2-layer simulation and more). Does it mean the model can compare now ? </div><div><br></div><div>Besides, the energy of the 1-layer and 2-layer and even more-layer simulation is nearly <span style="background-color: rgb(252, 252, 254); color: rgb(67, 67, 67); font-family: Arial, sans-serif; font-size: 14px;">geometric series. If energy of 1-layer is 1, then the energy of 2-layer is almost 2, and 3 of 3-layer. It makes me consider the energy belongs to the QM region. Hence, I want to know how to calculate the whole energy of the system.</span></div><div><span style="background-color: rgb(252, 252, 254); color: rgb(67, 67, 67); font-family: Arial, sans-serif; font-size: 14px;"><br></span></div><div><span style="background-color: rgb(252, 252, 254); color: rgb(67, 67, 67); font-family: Arial, sans-serif; font-size: 14px;">Or the geometric series is just a coincidence ? There is some mistake in my understanding ?</span></div><div><span style="background-color: rgb(252, 252, 254); color: rgb(67, 67, 67); font-family: Arial, sans-serif; font-size: 14px;"><br></span></div><div><span style="background-color: rgb(252, 252, 254); color: rgb(67, 67, 67); font-family: Arial, sans-serif; font-size: 14px;"><br></span></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br><br>在 2017年9月11日星期一 UTC+8上午12:19:07，Jadzia写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)">Hello again, </div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)"><br></div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)">in the case that you mean that you are using a different number of QM atoms, a significant energy difference can be expected. The reason is that different molecular models assign different energies to the same atoms/molecules. In particular QM atoms/molecules often have a much lower energy than MM atoms. QM models for instance usually include the electron-nuclei interactions explicitly while MM models do not, therefore you usually cannot directly compare the total energy of different molecular models even if the system is the same. If you shift the scale properly between the different models, then a comparison should be possible in theory, but I have not experience with that. </div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)"><br></div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)">Best wishes,</div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)">Jadzia</div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)"><br></div><div style="font-size:small;font-family:"trebuchet ms",sans-serif;color:rgb(32,18,77)"><br></div><br>On Sunday, September 10, 2017 at 5:24:40 PM UTC+2, <a>jts2...@gmail.com</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, Matt, bother you again. <div><br></div><div>The real problem I want to figure out is, when I set 1-layer QM atoms, the energy is</div><div>Total FORCE_EVAL ( QMMM ) energy (a.u.): -351.508815087281562</div><div><br></div><div>While I set 2-layer QM-atoms, the energy is </div><div>Total FORCE_EVAL ( QMMM ) energy (a.u.): -696.366434340290539</div><div><br></div><div>What bother me is that the energy should be almost the same, but the fact is that they differ nearly twice. </div><div>So I want to know if there is some mistake in my understanding, or is there some mistake in my setting ?<br><br>在 2017年9月8日星期五 UTC+8下午5:14:30，Matt W写道：<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">The line I suggested _is_ the total energy QM + MM + QM-MM<div><br></div><div>If you set print level medium you should see something like</div><div><br></div><div><div> QMMM| Evaluating forces on MM atoms due to the:</div><div> QMMM| - QM/MM Coupling computed collocating the Gaussian Potential Functions.</div><div> QMMM| QM/MM Nuclear Electrostatic Potential : -0.210189515</div><div> QMMM| QMMM Total Energy (QM + QMMM electronic + QMMM nuclear): -694.056114328</div><div> QMMM| MM energy NOT included in the above term! Check for: FORCE_EVAL ( QMMM )</div><div> QMMM| that includes both QM, QMMM and MM energy terms!</div><div><br></div><div> ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.): -696.223035107415399</div></div><div><br></div><div>Which gives the energy with and without the MM energy - so you can figure out the MM energy.</div><div><br><br>On Friday, September 8, 2017 at 6:45:52 AM UTC+1, <a>jts2...@gmail.com</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi, Matt,<div>Thanks for your advice! </div><div><br></div><div>I did as you suggest, then I typed in the command 'grep energy *.out'. But the results said </div><div><br></div><div>QMMM | MM energy NOT included in the above term! Check for: FORCE_EVAL(QMMM) that includes both QM, QMMM and MM energy terms !</div><div><br></div><div>So I still didn't get the MM energy message.</div><div><br></div><div>As far as my understanding, I should add something else in the &MM section, maybe an additional &FORCE_EVAL to output the information of MM region ?</div><div>Or there is something important ignored ?<br><br>在 2017年9月8日星期五 UTC+8上午4:16:40，Matt W写道：<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">At each step of a geo_opt run you should see something like<div><br></div><div>ENERGY| Total FORCE_EVAL ( QMMM ) energy (a.u.): -696.237954025524573<br></div><div><br></div><div>after all the QS output, that gives you the total energy of the system (at least if print_level is medium)<br><br>On Thursday, September 7, 2017 at 6:33:03 PM UTC+1, Jadzia wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>I am not sure if the question is really "where the file is" since it will most likely be nowhere. And to be honest I don't know how to write a similar file for the energies for geo_opt as for MD simulations since only in the MD section there seems to be this print option, which might not be used during geo_opt (not sure about it). </div><div><br></div><div>But a workaround might be as follows: One can run cp2k with the -o option to store the output of the geometry optimization in a file, and then one could grep the energy out of that file. </div><div><br></div><br><br>On Thursday, September 7, 2017 at 5:05:04 PM UTC+2, <a>jts2...@gmail.com</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for your suggestion, which works well in a example in official website, but fails in another case.<div><br><div>I run a GEO_OPT simulation using QMMM method, the original motion.inc is as follows</div><div><div>&MOTION</div><div> &GEO_OPT</div><div> OPTIMIZER LBFGS</div><div> &END</div><div> &CONSTRAINT</div><div> &FIXED_ATOMS</div><div> LIST 1..16</div><div> EXCLUDE_MM .TRUE.</div><div> EXCLUDE_QM .FALSE.</div><div> &END FIXED_ATOMS</div><div> &END CONSTRAINT</div><div>&END MOTION</div></div><div><br></div><div>Then I added the MD section, they became</div><div><div>&MOTION</div><div> &GEO_OPT</div><div> OPTIMIZER LBFGS</div><div> &END</div><div> &CONSTRAINT</div><div> &FIXED_ATOMS</div><div> LIST 1..16</div><div> EXCLUDE_MM .TRUE.</div><div> EXCLUDE_QM .FALSE.</div><div> &END FIXED_ATOMS</div><div> &END CONSTRAINT</div><div> &MD</div><div><span style="white-space:pre"> </span>&PRINT</div><div><span style="white-space:pre"> </span>&ENERGY</div><div><span style="white-space:pre"> </span> FILENAME=total.ener</div><div><span style="white-space:pre"> </span> &EACH</div><div><span style="white-space:pre"> </span> GEO_OPT 1</div><div><span style="white-space:pre"> </span> &END EACH</div><div><span style="white-space:pre"> </span>&END ENERGY</div><div><span style="white-space:pre"> </span>&END PRINT</div><div> &END MD</div><div>&END MOTION</div></div><div><br></div><div>The strange thing is that there wasn't any file named *total.ener* in the current directory. Where is the question ?</div><div>The &EACH section is not correct ?</div><div><br></div><div>Expect for your kind reply !</div><div><br></div><div><br></div><div><br><div><br>在 2017年9月7日星期四 UTC+8下午12:13:16，Jadzia写道：<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>To my understanding if you want to write the total energy to a file for instance for an MD simulation you need to add a section similar to:</div><div><br> &MOTION<br> &MD<br></div><div><div> &PRINT</div><div> &ENERGY</div><div> FILENAME =cp2k.out.energy</div><div> &EACH</div> MD 10<div> &END EACH</div><div> &END ENERGY</div><div> &END PRINT</div><div> &END MD</div></div><div>&END MOTION</div><div><br></div><div>In this example the energy of every tenth step is written to the file, and is independent of the type of force evaluation (MM, QM, QM/MM, ...). </div><div><br></div><div>Here is the corresponding section in the manual: <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD/PRINT/ENERGY/EACH.html" rel="nofollow" target="_blank" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FMOTION%2FMD%2FPRINT%2FENERGY%2FEACH.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEVg-AYx4ZC0HzxkrCtGN_Rf9YYuA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fmanual.cp2k.org%2Ftrunk%2FCP2K_INPUT%2FMOTION%2FMD%2FPRINT%2FENERGY%2FEACH.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEVg-AYx4ZC0HzxkrCtGN_Rf9YYuA';return true;">https://manual.cp2k.<wbr>org/trunk/CP2K_INPUT/MOTION/<wbr>MD/PRINT/ENERGY/EACH.html</a></div><div><br></div><div>Hope this helps,</div><div>Jadzia</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br>On Wednesday, September 6, 2017 at 8:31:10 AM UTC+2, <a>jts2...@gmail.com</a> wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear researchers and developers,<div><br><div>I am not so familiar with CP2K. After I run a QMMM simulation of KCl just as here: <a href="https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm" rel="nofollow" target="_blank" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.cp2k.org%2Fexercises%3A2017_ethz_mmm%3Aqmmm\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGiF0gJ6mRlaGSe7--tVuWgLftgjA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.cp2k.org%2Fexercises%3A2017_ethz_mmm%3Aqmmm\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGiF0gJ6mRlaGSe7--tVuWgLftgjA';return true;">https://www.cp2k.org/<wbr>exercises:2017_ethz_mmm:qmmm</a>, I want to know the energy of the whole system not just the energy of the QM region, how to achieve it in the input setting?</div><div><br></div><div>I'll appreciate for your apply !</div></div></div></blockquote></div></div></blockquote></div></div></div></div></blockquote></div></blockquote></div></div></blockquote></div></div></blockquote></div></div></blockquote></div></div></blockquote></div></blockquote></div></div>