<div dir="ltr"><div>From your last message I understand that you want to analyze this atoms and molecules in the gas phase. If this is correct, the box must be <span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">big enough for the PW basis and to ensure the molecule/atom does not interact with its own images if PBC is activated. A cubic cell of 15 Angstroms should be enough, if your system is a big molecule, a big cell may be necessary if PBC is activated.<br></span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">You need to do a Geometry Optimization to reach a minimum. In the case of Atoms, you do not need it, and with atoms you can not found vibrational modes. With an optimized geometry do the vibrational analysis.<br></span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-"><br></span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">The PBC is applied in the cases when you want to simulate a continuum system, as solids or liquids systems. If you want to simulate a big molecule in the gas phase, desactivate PBC.</span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-"><br></span></span></div><div><span class="gmail-tlid-translation gmail-translation" lang="en"><span title="" class="gmail-">Regards<br></span></span></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El vie., 17 ene. 2020 a las 7:39, sumit agrawal (<<a href="mailto:sumitag...@gmail.com">sumitag...@gmail.com</a>>) escribió:<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 Lucas Lodeiro,<div>Thanks for your response. Actually I want to do vibrational analysis in the matrix such as Ar and N2. So basically I want to make a cubic cell of the Ar or N2 and i want to put my molecule of interest inside this cube. So can you tell me what is the exact procedure to do such kind of calculations? Should I have to make a cubic cell first then optimized first and after optimization of this cubic cell I have to put my molecule of interest inside this and again I have to optimize this system? or simply should I make a system of interest and optimize this. </div><div><br></div><div>And one more inquiry I want that my interest in systems has less than 100 atoms so should I have to apply PBC of such kind of systems?</div><div><br></div><div>Thanks, Sumit<br><br>On Thursday, January 16, 2020 at 7:31:13 AM UTC-8, Lucas Lodeiro 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"><div>Hi Sumit,</div><div>If a vibrational mode presents a "negative" frequency (really it is an imaginary frequency, due to the hessian element is the negative one), it is because your system is not at minimmum stationary point (it could be in a 1° order saddle point). To fix it you must to do a geometry optimization first, to reach a stationary point, then a vibrational analysis will have useful information.</div><div>It is important to note that a vibrational analysis with Harmonic approximation does not have sense if you do not found a stationary point on the Potential Energy Surface.</div><div><br></div><div>Regards - Lucas Lodeiro<br></div></div><br><div class="gmail_quote"><div dir="ltr">El mar., 14 ene. 2020 a las 9:23, sumit agrawal (<<a rel="nofollow">sum...@gmail.com</a>>) escribió:<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">When I am trying to do to vibrational analysis, there are some modes that have negative frequencies. How can I solve this issue? </div>
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