<div dir="auto"><div dir="auto"></div>Ideally you need to use force field to optimize your structure classically. I do this for liquids.<div dir="auto">Then, you can continue NVE, T by quick step CP2K. Equilibration with AibMD is very time consuming, you will unlikely be able to equilibrate random structure with >300-500 atoms, or you could but it will be very expensive and long simulation. I couldn't equilibrate NPT of random liquid of 16*31+32*18+32 atoms with 36-48 cores for more than a month.</div><div dir="auto"><br></div><div dir="auto"> </div><div dir="auto"><br></div><div dir="auto"><br></div><div dir="auto"><br><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Mon, Nov 21, 2022, 1:18 AM jing liang <<a href="mailto:jingliang2015@gmail.com" target="_blank" rel="noreferrer">jingliang2015@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I am trying to see how the structure evolves in time, and monitor where some bond rotation occurs. The long story short, I<div>could pack all relevant molecules in a box. I was doing some search for parameters for gromacs/namd/... but I found it</div><div>not straightforward, also the mixing of force fields is something I am not completely sure about. Then, I thought that pure</div><div>CP2K simulation could work, and it is doing a great deal in the minimisation process. But I don't know how long it could</div><div>take to converge completely. </div><div><br></div><div>As I wrote before, the goal of this simulation would be to see if some bond rotation occurs in the long term some spectra</div><div>would be great but at this point just the dynamics. That's why I asked here if there is some standard/accepted criteria</div><div>for using a structure as the initial frame for an AI MD simulation regarding the energies/forces. Thanks for you comments. <br><div><div><br></div><div><br><br></div></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">El domingo, 20 de noviembre de 2022 a las 15:40:11 UTC+1, <a href="mailto:dresear...@gmail.com" rel="noreferrer noreferrer" target="_blank">dresear...@gmail.com</a> escribió:<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="auto">This is a good question but it depends on what you are simulating. If it is non- equilibrium system then it is pointless to look at the energy, temperature, pressure etc.<div dir="auto"><br></div><div dir="auto">If it is equilibrium system, it should be similar to classical MD but on a shorter time scale. There is a tutorial how to calculate IR spectra with cp2k, you can find steps there for equilibration and spectrum data acquisition. </div><div dir="auto">It is on cp2k website.</div><div dir="auto"><br></div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Nov 20, 2022, 5:33 PM jing liang <<a rel="nofollow noreferrer noreferrer">jingli...@gmail.com</a>> wrote:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<div><br></div><div>I created a simulation box manually and then started a minimisation process</div><div>by using geometry optimisation. My goal is not to get a fully optimised structure</div><div>but to start a MD simulation using the NVE ensemble. My question is if one needs</div><div>a fully optimised structure in order to start MD or if there is a criterion to say</div><div>that the minimised structure is already fine? </div><div><br></div><div>I am coming from classic MD simulations where some software suggest to have</div><div>the forces converged up to some particular threshold. </div><div><br></div><div>Thanks</div> <p></p></blockquote></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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 rel="noreferrer nofollow noreferrer noreferrer">cp2k+uns...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/7c1fb302-ae85-4a70-88d6-8dca9be6849en%40googlegroups.com?utm_medium=email&utm_source=footer" rel="noreferrer nofollow noreferrer noreferrer" target="_blank">https://groups.google.com/d/msgid/cp2k/7c1fb302-ae85-4a70-88d6-8dca9be6849en%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" rel="noreferrer noreferrer" target="_blank">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/8c294cd6-a99a-482c-8a84-304cbbbee083n%40googlegroups.com?utm_medium=email&utm_source=footer" rel="noreferrer noreferrer" target="_blank">https://groups.google.com/d/msgid/cp2k/8c294cd6-a99a-482c-8a84-304cbbbee083n%40googlegroups.com</a>.<br> </blockquote></div></div></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/CAG2SAD-6O8OLKT%2Bf%3D%2Bd6L5YiMx5-kAinE-tNHAdoepon2w5Svw%40mail.gmail.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/CAG2SAD-6O8OLKT%2Bf%3D%2Bd6L5YiMx5-kAinE-tNHAdoepon2w5Svw%40mail.gmail.com</a>.<br />