<div dir="ltr">Hi Dries,<div>    Thanks for you tutorial on biochemical systems. After seeing this tutorial ,I make some try on RNase systems. In order to save time ,I only chose four bases for simulation. But when I simulated a full QM/MM system, </div><div><br></div><div>I got the following error.</div><div><br></div><div>  *******************************************************************************</div><div><br></div><div><br></div><div>  Translating the system in order to center the QM fragment in the QM box.</div><div> WARNING| Particles:    5387     93 at distance [au]:     0.82969217 less than:      0.95400000; increase EMAX_SPLINE.</div><div><br></div><div> *******************************************************************************</div><div> *   ___                                                                       *</div><div> *  /   \                                                                      *</div><div> * [ABORT]                                                                     *</div><div> *  \___/                GEOMETRY wrong or EMAX_SPLINE too small!              *</div><div> *    |                                                                        *</div><div> *  O/|                                                                        *</div><div> * /| |                                                                        *</div><div> * / \                                               fist_neighbor_lists.F:607 *</div><div> *******************************************************************************</div><div>   I don't know why this problem occur .   Could you help me to see if there are any problems.</div><div>   </div><div>  For helping your understanding, I attach my files. Thank you in advance!</div><div>  </div><div>  Best wishes!</div><div>  </div><div>  Qing</div><div><br></div><div><div> 在 2017年7月18日星期二 UTC+8下午2:49:11，Dries Van Rompaey写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi cp2k-users, </div></blockquote><blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div><br></div><div>After experimenting with cp2k for a while I have written down a short tutorial on how to use cp2k for biochemical systems. The tutorial covers the setup of an enzyme system with ambertools followed by equilibration with cp2k at the MM level, after which we move the system to QM/MM for metadynamics simulations of an enzymatic reaction. I am far from an expert myself, but I thought this might be useful to people starting out. If you spot any mistakes or something that could be improved, please let me know. The tutorial can be found at <a href="https://driesvr.github.io/Tutorials/" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fdriesvr.github.io%2FTutorials%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHUfeTgDtfHSQQxB98lNzkiPh7cNw';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fdriesvr.github.io%2FTutorials%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHUfeTgDtfHSQQxB98lNzkiPh7cNw';return true;">https://driesvr.github.io/<wbr>Tutorials/</a> as well as on the main cp2k wiki: <a href="https://www.cp2k.org/howto:biochem_qmmm" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.cp2k.org%2Fhowto%3Abiochem_qmmm\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGFF6KZLn1b5lMS-l4pqtU0tRFBRA';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fwww.cp2k.org%2Fhowto%3Abiochem_qmmm\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGFF6KZLn1b5lMS-l4pqtU0tRFBRA';return true;">https://www.cp2k.org/<wbr>howto:biochem_qmmm</a>. </div><div><br></div><div>Kind regards</div><div><br></div><div>Dries</div><div><br></div><div><br></div></div></blockquote></div></div></div>