Dear Giacomo,<div><br /></div><div>thank you very much for your prompt reply and for your suggestion. </div><div><br /></div><div>I think that the strategy you are prosposing is useful for sure to have an idea about the contribution of the different bond vibrations to the normal modes of a specific conformer. However, I have still doubts concerning how to weight the NMA of the different conformers in order to interpret the whole IR spectrum. </div><div><br /></div><div>In particular, this would be important in case different conformers have different normal modes. I think that VDOS analysis could be useful as additional check, but information about the weights would be still missing</div><div><br /></div><div>However, I will try with your strategy and in the meanwhile I'll think about the next step.</div><div>Thank you very much for the stimulating discussion.</div><div><br /></div><div>Best regards,</div><div>Emma Rossi</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Il giorno giovedì 6 aprile 2023 alle 19:29:35 UTC+2 Giacomo Melani 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">Dear Emma,<div><br></div><div>You can certainly do a vibrational analysis through the standard input for such calculation (<a href="https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=it&q=https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html&source=gmail&ust=1680942598763000&usg=AOvVaw3WQJBqsVjBntYJlW2ZgDUo">https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html</a>). That will read your selected configuration and perform a diagonalization of the Hessian matrix to extract the corresponding normal mode frequencies and eigenvectors. This type of calculation will read a specific geometry. It can also provide you additional information, like IR/Raman intensities, but that requires the calculation of transition dipole moments and polarizabilities.</div><div><br></div><div>However, if you already have an AIMD trajectory, you might also want to do a vibrational analysis by computing a time correlation function. For instance, you can extract a vibrational density of states by calculating the time-autocorrelation function of nuclear velocities. For sure, the combination of NMA and correlation functions will give you the best assessment of vibrational modes in your system.</div><div><br></div><div>I hope this helps.</div><div><br></div><div>Best,</div><div><br>Giacomo Melani</div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno gio 6 apr 2023 alle ore 12:21 Emma Rossi <<a href data-email-masked rel="nofollow">emma.r...@studenti.unipd.it</a>> ha scritto:<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=1680942598763000&usg=AOvVaw0YaW6qySvNybf_YiCNdZVP">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> 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=1680942598763000&usg=AOvVaw3WLtBaRVTAw-I4X71qAaMl">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/e534f43c-6eeb-4d80-96bf-f7d9ecba2741n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/e534f43c-6eeb-4d80-96bf-f7d9ecba2741n%40googlegroups.com</a>.<br />