<div dir="ltr">Dear Huan,<div><br></div><div>I didn't display the trajectory, because the trajectory file is really big, thus it can't be dragged to VMD. I wrote a little program to identify it. First I found the min and max coordinates in the initial configuration, in ensemble NVT, when the atom coordinates less than min or larger than max, identify it crossing the boundary. And print out which atom and during which step.</div><div>Sure I can split the trajectory into several parts, but splitting costs too much time, and VMD always crash.</div><div><br></div><div>Best wishing,</div><div>Shengjie Wang <br></div><div>.<br>在 2016年3月24日星期四 UTC+8下午6:07:21，Huan Wang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 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><br></div><div>The codes are:</div><div><br></div><div>pbc set {xxx xxx xxx} -all </div><div><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>pbc box</div><div>pbc wrap -all </div><div><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><br></div><div>Good luck,</div><div>Huan</div><div>.</div><div><br><div class="gmail_quote">On Thu, Mar 24, 2016 at 3:39 AM, 王胜杰 <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="33kr2TMYJgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">theancientg...@gmail.<wbr>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>huan...@mail.<wbr>huji.ac.il</a>写道：<div><div><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" onmousedown="this.href='https://www.google.com/url?q\75https%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FCELL.html%23PERIODIC\46sa\75D\46sntz\0751\46usg\75AFQjCNFEtibqgWYDbJi0hfZ9rVUFLZpbOg';return true;" onclick="this.href='https://www.google.com/url?q\75https%3A%2F%2Fmanual.cp2k.org%2Fcp2k-2_6-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FCELL.html%23PERIODIC\46sa\75D\46sntz\0751\46usg\75AFQjCNFEtibqgWYDbJi0hfZ9rVUFLZpbOg';return true;">https://manual.cp2k.org/cp2k-<wbr>2_6-branch/CP2K_INPUT/FORCE_<wbr>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><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/A083JgzAgLo/unsubscribe" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/topic/cp2k/A083JgzAgLo/unsubscribe';return true;" onclick="this.href='https://groups.google.com/d/topic/cp2k/A083JgzAgLo/unsubscribe';return true;">https://groups.google.com/d/<wbr>topic/cp2k/A083JgzAgLo/<wbr>unsubscribe</a>.<br> To unsubscribe from this group and all its topics, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="33kr2TMYJgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp2k+uns...@googlegroups.<wbr>com</a>.<br> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="33kr2TMYJgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/group/cp2k';return true;" onclick="this.href='https://groups.google.com/group/cp2k';return true;">https://groups.google.com/<wbr>group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href='https://groups.google.com/d/optout';return true;" onclick="this.href='https://groups.google.com/d/optout';return true;">https://groups.google.com/d/<wbr>optout</a>.<br> </font></span></blockquote></div><br></div></div></div> </blockquote></div></div>