<div><br></div>Dear Ryan <div><br></div><div>The behaviour of the SCF is indeed very bad. </div><div>If possible, I would try to focus on the QM part only, simplify the model as much as you can, for instance using only one type of basis sets, and get it converged. </div><div>Kind regards</div><div>Marcella</div><div><br></div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Saturday, November 14, 2020 at 12:25:51 AM UTC+1 r...@nyu.edu wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr"><div>Dear Marcella,</div><div><br></div><div>Thank you very much for your suggestion. I tested removing the MM region, but unfortunately see similar behavior. <br></div><div>My configurations are generated from pure MM simulations with a custom force field which could possibly be allowing certain atoms to get a little too close. However, as the thermalized atom positions only vary (for the most part) by a few tenths of an Angstrom, no problematic close contacts can be found visually. <br></div><div><br></div><div>I've pasted below an example of the first SCF cycle from such a job, showing that the "Total energy" starts off much lower than I'm expecting (usually on the order of -2,000 +/- 500). During the SCF, the "Total energy" drops very low. When a job like this is allowed to continue, it won't crash on its own, but the "Total charge density on r-space grids" will become too large after 2-3 SCF cycles. <br></div><div><br></div><div>Is there any advice about how to handle atoms that are potentially "close" but not chemically "wrong"? These could potentially include hydrogen-bonding pairs like O-H, N-H, etc. <br></div><div><br></div><div>
<div>Any help is greatly appreciated in advance!<br></div></div></div><div dir="ltr"><div><div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">Sincerely,<br></font></div><div dir="ltr"><font color="#000000">Ryan Rogers<br></font></div><div dir="ltr"><font size="1" face="monospace, monospace" color="#000000"><a href data-email-masked rel="nofollow">r...@nyu.edu</a></font><div><div><font color="#000000">~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></div></div></div></div></div></div></div></div></div></div></div>
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<span style="font-family:monospace">################################################################################<br> SCF WAVEFUNCTION OPTIMIZATION<br><br> ----------------------------------- OT ---------------------------------------<br> Minimizer : DIIS : direct inversion<br> in the iterative subspace<br> using 7 DIIS vectors<br> safer DIIS on<br> Preconditioner : FULL_ALL : diagonalization, state selective<br> Precond_solver : DEFAULT<br> stepsize : 0.15000000 energy_gap : 0.00100000<br> eps_taylor : 0.10000E-15 max_taylor : 4<br> ----------------------------------- OT ---------------------------------------<br><br> Step Update method Time Convergence Total energy Change<br> ------------------------------------------------------------------------------<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 1 OT DIIS 0.15E+00 66.7 0.13322879 -8451.7456190410 -8.45E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 2 OT DIIS 0.15E+00 65.4 0.13364185 -10643.9042780022 -2.19E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 3 OT DIIS 0.15E+00 65.7 0.15497766 -13025.7969156521 -2.38E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 4 OT DIIS 0.15E+00 65.5 0.14868108 -14464.8777105315 -1.44E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 5 OT SD 0.15E+00 65.5 0.17759857 -14843.1753581151 -3.78E+02<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 6 OT DIIS 0.15E+00 65.8 0.32256964 -13383.1417204580 1.46E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 7 OT DIIS 0.15E+00 65.6 0.19569799 -14813.0440620911 -1.43E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 8 OT DIIS 0.15E+00 65.3 0.24452346 -15865.0025958057 -1.05E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 9 OT DIIS 0.15E+00 65.5 0.26678603 -14795.2757334147 1.07E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 10 OT DIIS 0.15E+00 65.7 0.36307397 -17004.3658543152 -2.21E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 11 OT DIIS 0.15E+00 65.6 0.48782211 -17176.2139668702 -1.72E+02<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 12 OT DIIS 0.15E+00 65.5 0.45773260 -15669.9100288352 1.51E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 13 OT DIIS 0.15E+00 65.5 0.66194382 -18842.9056350951 -3.17E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 14 OT DIIS 0.15E+00 65.6 0.63269527 -16132.4918799441 2.71E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 15 OT DIIS 0.15E+00 65.7 0.73064928 -16834.2508612376 -7.02E+02<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 16 OT DIIS 0.15E+00 65.5 1.15829587 -27460.2661838299 -1.06E+04<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 17 OT DIIS 0.15E+00 65.7 0.70782891 -15281.5935133825 1.22E+04<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 18 OT DIIS 0.15E+00 65.7 0.98480536 -20548.0516400897 -5.27E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 19 OT DIIS 0.15E+00 65.6 1.39954759 -33842.8143338371 -1.33E+04<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 20 OT DIIS 0.15E+00 65.6 1.33809404 -29354.7460547364 4.49E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 21 OT DIIS 0.15E+00 65.4 1.62600866 -36147.2741396100 -6.79E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 22 OT DIIS 0.15E+00 65.6 1.21990609 -24956.2600892884 1.12E+04<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 23 OT DIIS 0.15E+00 65.6 1.32400959 -27440.1826004675 -2.48E+03<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 24 OT DIIS 0.15E+00 65.5 1.81006425 -42812.1680574805 -1.54E+04<br> Adding QM/MM electrostatic potential to the Kohn-Sham potential.<br> 25 OT DIIS 0.15E+00 65.7 0.89367434 -18701.9345340245 2.41E+04<br><br> Leaving inner SCF loop after reaching 25 steps.<br><br><br> Electronic density on regular grids: -1218.0000000005 -0.0000000005<br> Core density on regular grids: 1217.9999999992 -0.0000000008<br> Total charge density on r-space grids: -0.0000000013<br> Total charge density g-space grids: -0.0000000013<br><br> Overlap energy of the core charge distribution: 0.00009990728015<br> Self energy of the core charge distribution: -4772.82460287547656<br> Core Hamiltonian energy: 2367.11980010682919<br> Hartree energy: -15786.54494725671611<br> Exchange-correlation energy: -509.06361063631039<br> Dispersion energy: -0.62127327012014<br> QM/MM Electrostatic energy: 0.00000000000000<br><br> Total energy: -18701.93453402451269<br><br> outer SCF iter = 1 RMS gradient = 0.89E+00 energy = -18701.<a href="tel:(934)%20534-0245" value="+19345340245" target="_blank" rel="nofollow">9345340245</a><br>################################################################################
</span><br></div><div><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><font color="#000000"></font></div></div></div></div></div></div></div></div></div></div><br></div></div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 5, 2020 at 10:20 AM Женя Елизарова <<a href data-email-masked rel="nofollow">zh...@gmail.com</a>> wrote:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I see.<div> Actually, I would like to know is it possible to run a single point energy calculation of the QM subsystem without the removal of the MM part, not in relation to the previous posts (in general)?<div><br></div><div><br></div><div>Best wishes,</div><div>Evgenia<br><br></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">четверг, 5 ноября 2020 г. в 19:08:44 UTC+3, Marcella Iannuzzi: <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>Dear Evgenia Elizarova<div><br></div><div>Is this question related to the previous posts in this conversation? </div><div>If yes, what I meant is to remove all the MM part and just carry out a DFT calculation of the QM part. </div><div>Regards</div><div>Marcella</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, November 5, 2020 at 3:29:42 PM UTC+1 <a rel="nofollow">zh...@gmail.com</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>Dear
Marcella Iannuzzi<div><br></div><div>I've just started to explore opportunities of the cp2k package. I've done some tutorials about single-point calculations of ethane molecule, QM/MM simulations, and some more. I am very interested in single point energy calculation for the QM part of the system. As I understood, I have to define the force_eval section (method - quickstep), and also I have to define subsections: dft, subsys, qmmm. Did I understand correctly? Also, i have some questions.</div><div>Do I have to define the MM subsection? In subsys section, I should define the whole system? How to define for which part of the system run a single point calculation?</div><div> Could you help me, please?</div><div><br></div><div>Best wishes, </div><div>Evgenia Elizarova</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">понедельник, 2 ноября 2020 г. в 11:55:28 UTC+3, Marcella Iannuzzi: <br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Ryan Rogers<div><br></div><div>There is apparently a problem with the conservation of the charge on the QM grid. </div><div><br></div><div>Did you try to run a single point energy calculation for the QM part alone?</div><div>Kind regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, October 29, 2020 at 7:11:42 PM UTC+1 <a rel="nofollow">r...@nyu.edu</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I might add that I have not been able to identify any obvious problems with the configurations (e.g. overlapping or too close atoms, etc.) when I encounter these errors. <br><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, October 26, 2020 at 4:07:46 PM UTC-5 Ryan Rogers wrote:<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"><a rel="nofollow"></a><div>Dear CP2K community, <br></div><div><br></div><div>I am having issues in DFT QM/MM force calculations on molecular crystals of paracetamol (acetaminophen). I am describing here the two problems I most often experience.
I am currently unable to identify the cause or any pattern in the problems I encounter.
The root of the problems could be something other than what I identify below; I am pointing out the problematic features in the output that are most obviously to me. All input and output files are included. <br></div><div><br></div><div><b>1. Total energy falls into "hole" and never converges. (CP2K_problemTotalE_conf_0636.tar.gz)</b><br></div><div>Personal experience tells me to expect a "Total energy" for these systems on the order of -2,000 (Hartree) and a "Hartree energy" on the order of +2,000 (Hartree).<br></div><div>In these jobs, I find an initial "Hartree energy" on the order of >-10,000 (Hartree), which appears to send the SCF wavefunction optimization down a path of non-convergence, in which the "Total energy" can easily become on the order of -100,000 (Hartree) before I kill the job.</div><div><br></div><div><b>2. Total charge density on grids grows too large. (CP2K_problemEGrids_conf_0623.tar.gz)</b><br></div><div>In these jobs, the Total energy looks reasonable, and the Convergence looks promising in the few SCF cycles of steps. <br></div><div>However, the total Change never drops below my threshold, and eventually the "Total charge density on r-space/g-space grids" becomes much too large.<br></div><div><br></div><div>
My configurations are extracted from MD trajectories, so the atoms have perturbations from their perfect crystal positions. One confusing observation is that very similar QM/MM configurations selected from other frames of the same trajectory often have no problems.</div><div>My configurations are constructed from a cluster of several molecules in the QM region with usually another layer usually 1-2 molecules thick making up the MM region. (In the attached sample images, the size of the stick molecules alludes to a larger/smaller basis set used, while the MM atoms are denoted as points.) Because I am not including integer numbers of unit cells, I am not using PBC. <br></div><div><br></div><div>Any advice about both/either problem will be greatly appreciated!<br></div><div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font color="#000000"><br></font></div><div dir="ltr"><font color="#000000">Sincerely,<br></font></div><div dir="ltr"><font color="#000000">Ryan Rogers<br></font></div><div dir="ltr"><font size="1" face="monospace, monospace" color="#000000"><a rel="nofollow">r...@nyu.edu</a></font><div><div><font color="#000000">~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></div></div></div></div></div></div></div></div></div></div></div></div>
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