<div dir="ltr">Dear Prof.Travis<div><br></div><div>Thank you very much for your help and patience.It works now.</div><div><br></div><div>Have a nice day</div><div>Best regards</div><div><br></div><div>Liyi</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Travis <<a href="mailto:polla...@gmail.com">polla...@gmail.com</a>> 于2019年12月15日周日下午7:05写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>You've just loaded your coordinates incorrectly. Load XYZ first. Right click the line <a href="http://water-1.xyz" target="_blank">water-1.xyz</a>, select Load Data Into Molecule. Ensure <a href="http://water-1.xyz" target="_blank">water-1.xyz</a> is the molecule that is selected in the drop down menu. The default option in the Load Menu is to create a new molecule. Now just load the DCD. You will have a total number of frames equal to the number of frames in the DCD + 1 for the XYZ. You can print also to PDB which includes lattice, coordinate, and atom name data but sacrifices some precision as it writes fewer decimal places.</div><div><br></div><div>-T</div><div><br><br>On Sunday, December 15, 2019 at 2:20:00 AM UTC-5, lizzy bai wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear Prof.Travis<div><br></div><div>Thank you very much for you reply.</div><div>Sorry, I have understood your points? "Convert the coordinates in your input file to XYZ." Here what kind of input are you mentioning?</div><div><br></div><div>I tried load the DCD and then load the xyz file. Then the the VMD displayed like below.</div><div>Previously, I tried load the lammps output DCD file along with the psf file, it woks well.</div><div>But for the cp2k output DCD, it doesn't work.</div><div>And, may I know it is possible to output both DCD and xyz files in CP2K?</div><div><br></div><div><br></div><div>Thank you very for your help</div><div><br></div><div>best regards</div><div><br></div><div>Liyi</div><div><br></div><div><div><img src="https://groups.google.com/group/cp2k/attach/16507e6121763/WeChat%20Image_20191215160944.png?part=0.1&view=1&authuser=0" alt="WeChat Image_20191215160944.png" width="464" height="210"><br></div></div></div><br><div class="gmail_quote"><div dir="ltr">Travis <<a rel="nofollow">po...@gmail.com</a>> 于2019年12月14日周六下午5:19写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>Convert the coordinates in your input file to XYZ. You need only a single snapshot. Then load the XYZ into VMD and select to load additional data into the molecule to append the DCD. The XYZ file is used just to add the atom names. You can also use one of the snapshots from your old XYZ trajectory to do this.</div><div><br></div><div>-T</div><div><br><br>On Saturday, December 14, 2019 at 3:04:56 AM UTC-5, lizzy bai wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear Prof. Travis<div><br></div><div>Thank you very much for you information.</div><div>I have formated the trajectory as DCD. Then the outfile only has DCD file, no xyz file. The following keywords I used as below:</div><div> &TRAJECTORY</div><div> FORMAT DCD<br> &EACH<br> MD 1<br> &END EACH<br> &END TRAJECTORY<br></div><div><br></div><div>Best regards</div><div><br></div><div>Liyi</div></div><br><div class="gmail_quote"><div dir="ltr">Travis <<a rel="nofollow">po...@gmail.com</a>> 于2019年12月13日周五下午10:45写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<br> <br> You load an XYZ first. Then load DCD as additional data. DCD doesn't contain atom names.<br> <br> -T<br> <br> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">c...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/99e88dd0-a25f-4b2c-8f2b-92afd080e603%40googlegroups.com" rel="nofollow" target="_blank">https://groups.google.com/d/msgid/cp2k/99e88dd0-a25f-4b2c-8f2b-92afd080e603%40googlegroups.com</a>.<br> </blockquote></div> </blockquote></div></div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">c...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/74387394-44cc-483b-bb1b-c6120f36b1ec%40googlegroups.com?utm_medium=email&utm_source=footer" rel="nofollow" target="_blank">https://groups.google.com/d/msgid/cp2k/74387394-44cc-483b-bb1b-c6120f36b1ec%40googlegroups.com</a>.<br> </blockquote></div> </blockquote></div></div> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/539a0b8a-dad7-4ac4-b32e-6a37b72f81c7%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/539a0b8a-dad7-4ac4-b32e-6a37b72f81c7%40googlegroups.com</a>.<br> </blockquote></div>