<div dir="ltr"><div>Hi,</div><div> </div><div>The file I generated looks like this,</div><div><div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint">TITLE Gromos96 structure file written by ASE END POSITION 1 DUM O 1 -0.466435441 0.134996386 -0.513981110 1 DUM H 2 -0.456093036 0.106021788 -0.419837619 1 DUM H 3 -0.420027567 0.062658494 -0.564346835 1 DUM O 4 0.115815785 0.219921049 0.557675443 1 DUM H 5 0.141607659 0.194800907 0.467369599 1 DUM H 6 0.041911702 0.157741781 0.572592000 1 DUM O 7 0.260380086 0.630856816 -0.541834739 1 DUM H 8 0.357742539 0.651611259 -0.535899313 1 DUM H 9 0.271335808 0.537091104 -0.513030977 END BOX 91.500000000 25.800000000 19.100000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 END </div></code></div> The atoms are colored by the name in column 3 and can be selected by 'name O' and so on. DUM is probably a molecule or force field tag.</div><div> </div><div>As to your second point - did you output cell parameters at the same frequency as coordinates? If not, you would need to adjust the script to ignore the frames without parameters (index=':' is the only thing you would need to change). There's nothing in the Python code that limits the number of frames. It just assumes that the number of frames and the number of entries in .cell are equal. </div><div> </div><div>-T </div><div> </div> On Friday, October 25, 2019 at 1:03:22 PM UTC-3, Ant wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div>Travis, I used your code with my .cell file and trajectory (.xyz) files--thank you. Would you happen to have time for a couple of follow-up questions on this?</div><div> </div><div>1. It generated an output file like the one at the end of this message. When I read it into VMD, it seemed to show all atoms as identical (i.e., the atom types are not distinguished). I'm guessing this has something to do with the first and second columns. I can't find an example online of what they should be. </div><div> </div><div>2. Another problem is that the output file only contains about 300 time steps. This may not be something you can help with, but I thought I would mention it just in case. Thank you again very much. </div><div> </div><div>TITLE Gromos96 structure file written by ASE END POSITION 1 DUM Ar 1 0.271226802 1.105695742 0.687656962 1 DUM Ar 2 0.171226802 0.705695742 0.287656962 1 DUM Cl 3 0.987788274 0.553369424 0.340889882 1 DUM Cl 4 1.017388949 1.095946397 1.012254758 1 DUM O 5 0.171226802 1.056957424 0.287656962 1 DUM O 6 0.087788274 -0.053369424 0.040889882 1 DUM H 7 0.017388949 0.695946397 -0.212254758 1 DUM H 8 -0.809217934 0.646737810 0.262515118 ...</div><div> ... </div><div>END BOX 1.361050000 1.361050000 1.361050000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 END</div></div> </blockquote></div>