<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 zh...@gmail.com 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;"><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:0 0 0 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:0 0 0 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:0 0 0 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" data-smartmail="gmail_signature"><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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