Dear Lucas,<div><br /></div><div>Thank you very much for your suggestion. I obtained the IR spectrum through the dipole moment of the whole box computed at each step of the trajectory by CP2K. Unfortunately, I couldn't use TRAVIS since I had not printed the electron density during the simulation.</div><div><br /></div><div>However, it would be great if I could use TRAVIS as post processing tool to perform NMA on the trajectory. As far as I have seen in the documentation, the online tutorials/presentations deal only with the simulation of the spectra, which, indeed, require electron density. I couldn't find any instruction about how to perform the NMA (I've found just the original paper). </div><div><br /></div><div>However, if you have expertise in TRAVIS usage, I would be very grateful if you could answer a doubt about TRAVIS NMA tool.</div><div><br /></div><div>Can I perform NMA on my trajectory without performing as a preliminary step the calculation of the IR spectrum? As I mentioned above, I have not the electron density.</div><div><br /></div><div>Thank you very much for your kind support.</div><div><br /></div><div>Best regards,</div><div>Emma Rossi</div><div><br /></div><div><br /></div><div><br /></div><div><br /></div><div><br /><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Il giorno giovedì 6 aprile 2023 alle 23:59:45 UTC+2 Lucas Lodeiro ha scritto:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr">Hi Emma,<div><br></div><div>I do not know how you managed to obtain the IR spectrum from your trajectory, but I suggest the TRAVIS program to do it: <a href="http://www.travis-analyzer.de/" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=it&q=http://www.travis-analyzer.de/&source=gmail&ust=1680946696165000&usg=AOvVaw24Fadn_Ro7BNZoaYF_pmj3">http://www.travis-analyzer.de/</a></div><div>There is many ways to accomplish it, and the results are very good. Also, there is the possibility to obtain the "normal modes" of the trajectory which are consistent with the trajectory IR/Power spectrum.</div><div>There are some tutorials, and the program is self explaining: <a href="https://brehm-research.de/spectroscopy.php" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=it&q=https://brehm-research.de/spectroscopy.php&source=gmail&ust=1680946696165000&usg=AOvVaw1-cU3YKVgVq_X4TaBcpkWE">https://brehm-research.de/spectroscopy.php</a></div><div><br></div><div>In the normal modes section you can feed the program with one or more minimum energy conformer where the trajectory is projected, and approximated normal modes are obtained.</div><div><br></div><div>Regards - Lucas</div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 6 abr 2023 a las 14:21, Emma Rossi (<<a href data-email-masked rel="nofollow">emma.r...@studenti.unipd.it</a>>) escribió:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear all,<div><br></div><div>I would need to assign the bands of an IR spectrum, obtained through AIMD simulation. </div><div><br></div><div>I would like to perform a normal mode analysis (NMA) on the trajectory I have already produced to properly take into account solvation effects as well as the correct weight of the sampled conformers. </div><div><br></div><div>I guess I could do so retracing the <a href="http://traj.xyz" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=it&q=http://traj.xyz&source=gmail&ust=1680946696165000&usg=AOvVaw0l-wg9_KACl3kWbiG1KFOZ">traj.xyz</a> and using the vibrational analysis section in the input, but I would be very greatful if you could clarify a few issues about this strategy:<br></div><div><br></div><div>1) is it the most efficient and correct way to do NMA over a trajectory or do you suggest any other ways?</div><div><br></div><div>2) how the output with eigenfrequencies and eigenvectors should look like? I can figure the typical output for NMA on single configurations, but I have no ideas of what should I expect for NMA on trajectories (I suppose that the hessian will be diagonalized at each step, but how these info will be put together at the end of the process? )</div><div><br></div><div>I have read the original paper of CP2K and the pdf presentations available online, but I couldn't fix my problem.</div><div><br></div><div>I am very willing to understand and learn from anyone who will help.</div><div><br></div><div>Thank you very much in advance for your support.</div><div><br></div><div>Best regards,</div><div>Emma Rossi</div> <p></p></blockquote></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> -- <br></blockquote></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> 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 data-email-masked rel="nofollow">cp2k+uns...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/6edca95f-7fb7-4a27-97cd-5868c9ae611en%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=it&q=https://groups.google.com/d/msgid/cp2k/6edca95f-7fb7-4a27-97cd-5868c9ae611en%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1680946696165000&usg=AOvVaw00YqB8Tp9yGN6_ffZoIwyX">https://groups.google.com/d/msgid/cp2k/6edca95f-7fb7-4a27-97cd-5868c9ae611en%40googlegroups.com</a>.<br> </blockquote></div></blockquote></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:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/6bc02dbb-0824-46a7-8edc-8d98c5c87f21n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/6bc02dbb-0824-46a7-8edc-8d98c5c87f21n%40googlegroups.com</a>.<br />