<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">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 dir="ltr" class="gmail_attr">Il giorno gio 6 apr 2023 alle ore 12:21 Emma Rossi <<a href="mailto:emma.rossi.1@studenti.unipd.it">emma.rossi.1@studenti.unipd.it</a>> ha scritto:<br></div><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">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>
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