<div dir="ltr">It seems that such modification will not change a lot in the results. <div>You can have a try.</div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-18 1:33 GMT-05:00 <span dir="ltr"><<a href="mailto:jts2t...@gmail.com" target="_blank">jts2t...@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello William, I want to know the influence of the change from {<b>38.8605230 39.1154930 39.2709120</b>} to {<b>22.564 22.699 22.781</b>}. Does the output change a lot?<br><br>在 2017年4月6日星期四 UTC+8下午11:57:16，William Tao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>Now I have understood much better for my own problems.</div><div><br></div><div>1) The cell size (ABC) for the 1st step MM Equilibrium is too large. I guess the author didn't convert the {<b>38.8605230 39.1154930 39.2709120</b> } which is in the unit of Bohr into Angstrom. So, right now I changed this into "<b>ABC 22.564 22.699 22.781</b>". </div><div><br></div><div>2) NPT then NVT, now it is clear to me.</div><div><br></div><div><br></div><div>Please correct me if I am wrong, especially with regard to the (1) question.</div><div><br></div><div><br></div><div>William</div><div><br></div><br><br>在 2017年3月21日星期二 UTC-5下午9:21:57，William Tao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 World,<div><br></div><div>I have been learning cp2k calculation with tutorials on the website. And I have a few questions about the tutorial by Professor Iannuzzi, "<a href="https://www.cp2k.org/exercises:2015_cecam_tutorial:urea#fourth_taskqm_mm_metadyanamics_simulations" rel="nofollow" target="_blank">QM/MM study of UREA Zwitterion in water</a>".</div><div><br></div><div>1) In the first task of "First task: MM isobaric/isothermal ensemble", the cell size is specified as "ABC [angstrom] 38.8605230 39.1154930 39.2709120", I do not know where these numbers are from. I measured the initial length of the cubic box generated from ambertools, it is around only 20 angstroms.</div><div><br></div><div>2) The second question is about the procedure of calculation. We do the NPT in the first step, why do we need to do the following NVT ensemble in the second and third step?</div><div><br></div><div>3) How to correctly visualize the result of step 1(The NPT ensemble) in VMD?(I saw the whole system seems to be shifting here and there) Should we expect a rectangular unit cell for the whole system? Does CP2K have the functionality of "wrap" that can move atoms outside the unit cell back into the box? <br></div><div><br></div><div>I really appreciate that many professors and developers contributed to these helpful tutorials. </div><div><br></div><div>If anyone can answer these questions, it would be fantastic.</div><div><br></div><div>Thanks.</div><div><br></div><div>William</div><div><br></div><div><br></div><div><br></div></div></blockquote></div></blockquote></div><span class="HOEnZb"><font color="#888888"> <p></p> -- <br> You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br> To unsubscribe from this topic, visit <a href="https://groups.google.com/d/topic/cp2k/L_Ltmg3ohsk/unsubscribe" target="_blank">https://groups.google.com/d/<wbr>topic/cp2k/L_Ltmg3ohsk/<wbr>unsubscribe</a>.<br> To unsubscribe from this group and all its topics, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+unsubscribe@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/<wbr>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/<wbr>optout</a>.<br> </font></span></blockquote></div><br></div>