<div dir="ltr">Hi Shengjie,<div><br></div><div>An additional question is how do you display the trajectory? </div><div>If you use VMD, then you need to type some codes in <b>Extensions --> Tk console</b> to let the VMD know the size of your simulation box.<br><div class="gmail_extra"><br></div><div class="gmail_extra">The codes are:</div><div class="gmail_extra"><br></div><div class="gmail_extra">pbc set {xxx xxx xxx} -all </div><div class="gmail_extra"><font color="#0000ff"># Here the "xxx" is the length of your (cubic) box</font>. <font color="#0000ff">And "-all" means this operation controls all frames in the current trajectroy.</font></div><div class="gmail_extra">pbc box</div><div class="gmail_extra">pbc wrap -all </div><div class="gmail_extra"><font color="#0000ff"># The wrap commend will show the atoms on the other side of the box when atoms move out of the box.</font></div><div class="gmail_extra"><br></div><div class="gmail_extra">Good luck,</div><div class="gmail_extra">Huan</div><div class="gmail_extra">.</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 24, 2016 at 3:39 AM, 王胜杰 <span dir="ltr"><<a href="mailto:theancientg...@gmail.com" target="_blank">theancientg...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Huan,<div><br></div><div>Thanks for your attention.</div><div>Yes, I did. I noticed and added the keyword the PERIODIC, and I tried the ensemble NPT_I and NVT, but cp2k still printed a real trajectory.</div><div><br></div><div>Regards,</div><div>Shengjie Wang<br><br>在 2016年3月23日星期三 UTC+8上午4:45:33，<a href="mailto:hua...@mail.huji.ac.il" target="_blank">hua...@mail.huji.ac.il</a>写道：<div><div class="h5"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Shengjie,<div><br></div><div>Did you specify the keyword PERIODIC in the &SUBSYS &CELL section?</div><div>Please see the CP2K manual</div><div> <a href="https://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#PERIODIC" rel="nofollow" target="_blank">https://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#PERIODIC</a><br><br>Regards,</div><div>Huan</div><div>.<br><br>On Friday, March 18, 2016 at 6:41:41 PM UTC+2, 王胜杰 wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Dear all<div><br></div><div>When I was dealing with the trajectory of MD, I found the atoms always move beyond the boundary, making some atoms' coordinate larger than the box length,which reflect the true trajectories. </div><div>But I don't want a true trajectory, I want a periodic boundary.When the atoms cross the boundary, the coordinate will minus the box length automatically, which each direction of atoms' coordinate is less than the box length. By adding what command line can I fix that?</div><div><br></div><div>Thanks in advance.</div><div>Shengjie Wang </div></div></blockquote></div></div></blockquote></div></div></div></div><span class=""><font color="#888888">
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