<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: -webkit-standard; font-size: medium;">Dear Yibo Wang, </span><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><br /></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">I cannot say whether the simulation is reasonable now. </div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">If the initial forces obtained from a not converged electronic structure calculation are very wrong, it is possible that the system ended up in an unphysical structure from which it will never come back. Or maybe not.</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Anyway, it would be for sure much better to run a stable MD with your new system, before running metadynamics.</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">It is indeed very important to monitor the sampling of the configurational space with an unbiased dynamics to be able to define useful collective variables and to set the reasonable parameters. </div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">In addition to that, I strongly suggest to also read review papers on metadynamics before starting using it, such that you can decide which type of approach is best suitable for your system.</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">For instance the lambda and mass parameters are only needed for a lagrangian metadynamics. Are you sure that you are using this option? And if yes, are you sure that this is the optimal choice for your needs?</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">You also have a wall in your definition. How can you set it before knowing which is the unbiased behaviour of the collective variable?</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><br /></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Unfortunately metadynamics, as most of the methods in molecular simulations, is not just a black box tool, you need to know very well what you are doing to avoid generating unreliable results. </div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><br /></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Regards,</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);">Marcella</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"><br /></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);"></div><br style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" /><br /><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, March 22, 2023 at 9:50:02 AM UTC+1 yibowang333 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;">
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<span>Dear <span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none">Marcella</span>
</span></div><div><span><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"><br></span></span></div><div><span><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none">First of all thanks a lot for your help.</span></span></div><div><span><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"><br></span></span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">The water molecules in the system are copied directly from a previous aimd simulation that has been balanced. I just replaced the metal atoms supported in the previous C2N graphene. This may lead to its unreasonable initial structure and slow convergence. In fact ,the trajectory file actually started output after I sent the email shortly. However, there is a reminder <span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none">"WARNING in qs_scf.F:598 :: SCF run NOT converged"</span> in the output file , but the subsequent SCF operations have converged (Sometimes I also encounter this situation when doing geometry optimization). Are the results credible in this case?</span><br></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"><br></span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">In addition, I also think that the slow operation may be caused by the unreasonable parameter setting in the input file. I don't quite understand the meaning of the keywords LAMBDA and MASS under the METAVAR scetion. I just learned from your lecture on YouTube that their unit changes with the unit of CV.I don't know their specific impacts of the system while doing metadynamics(maybe of my poor English listening?). I want to know if it is reasonable to set such a setting with reference to the parameters in your course ppt.</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &METAVAR
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> COLVAR 1
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> SCALE 0.2
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> LAMBDA 0.8
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> MASS 20
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &WALL
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> POSITION 5.0
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> TYPE QUADRATIC
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &QUADRATIC
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> DIRECTION WALL_MINUS
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> K 0.5
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &END QUADRATIC
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &END WALL
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"> &END METAVAR
</span></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"><br></span></div><div><br></div><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">Appreciate again for your help!</span></div></div></div></div><div><div style="font-family:微软雅黑,Verdana,"Microsoft Yahei",SimSun,sans-serif;font-size:14px;line-height:1.6"><div style="font-family:微软雅黑;font-size:14px;line-height:1.6"><div><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px"><br></span></div><div><div style="font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;word-break:break-word!important"><span style="line-height:22.4px">Sincerely,</span><br></div><div style="font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;word-break:break-word!important">Yibo Wang</div></div><div>
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<a style="color:#3061f2;text-decoration:none" href data-email-masked rel="nofollow">Marcella Iannuzzi<marci...@gmail.com>
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cp2k<cp...@googlegroups.com>
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[CP2K:18575] Re: Problems about doing metadynamics of CO2 adsorption
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Dear <span style="color:rgb(49,53,59);font-family:Verdana,"Microsoft Yahei",SimSun,sans-serif">Yibo Wang</span><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif"><span><br></span></font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif">If there is no MD output most probably the electronic structure optimization at the very first step is not converging. </font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif">If this is the case, one should first work on the electronic structure settings.</font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif">Could you run ab initio MD without metadynamics for the same system?</font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif"><br></font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif">Regards</font></div><div><font color="#31353b" face="Verdana, Microsoft Yahei, SimSun, sans-serif">Marcella</font></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, March 22, 2023 at 2:29:43 AM UTC+1 yibowang333 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">
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<span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">Dear </span><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">users and developers</span><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px">,</span><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"> </div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"> I want to do a metadynamic test of CO2 adsorption on a C2N graphene, but I found that there is still no output trajectory file after running for nearly 15 hours. I chose the distance from an O atom(in red color) and C atom(in gray color) in the CO2 molecule to the Fe atom(in green color) on the substrate as the CV. I think this setting should be reasonable. I wrote the following input file with reference to the ppt on the official course, but I don't know if it is accurate. In addition, I don't quite understand the meaning of the parameters in lambda, mass and WALL in the metavar module. I hope I can get an explanation if possible. Below is my <span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none">input file,the </span>initial structure, and the final state I want to have.</div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"><br></div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"></div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"><span style="line-height:22.4px"><span style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:22.4px;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"> Appreciate</span> a lot for your help!</span><br></div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"><span style="line-height:22.4px"><br></span></div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important"><span style="line-height:22.4px">Sincerely,</span><br></div><div style="color:rgb(49,53,59);font-family:Verdana,'Microsoft Yahei',SimSun,sans-serif;line-height:22.4px;word-break:break-word!important">Yibo Wang</div><span>
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