<div>First of all, how big (no. of atoms) is your system?</div><div><br></div><div>If it is fairly small (around 500 -700 atoms with some 80 processors) then you can try to attempt AIMD simulation.</div><div><br></div><div>Best thing, I found, to start an AIMD simulation is to run a few pico seconds (may be 100-200 ps) classical simulation with a reasonable force field.</div><div>Then start your AIMD from the last step configuration.</div><div><br></div><div>Best of luck.</div><div><br></div><div>N Choudhury<br></div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, November 21, 2022 at 2:17:54 PM UTC+5:30 jingli...@gmail.com wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thank you for your useful comments, I am starting to think about returning to namd/gromacs. But before<div>I do it, I wanted to ask you what criteria do you use to find out whether the system is equilibrated or not. </div><div>I found this page <a href="https://www.cp2k.org/howto:md?do=" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.cp2k.org/howto:md?do%3D&source=gmail&ust=1669110976089000&usg=AOvVaw2-lrEkkpHHJYDMvh-3NNKQ">https://www.cp2k.org/howto:md?do=</a> From it, I understood that by looking at the column</div><div>"Cons Qty[a.u.]" from the .ener file, one could get the difference between the maximum and minimum of the</div><div>curve and divide it by the kinetic energy, for an equilibrated system this ratio should be < 1% Maybe I didn't</div><div>get the point? </div><div><br></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">El lunes, 21 de noviembre de 2022 a las 0:38:09 UTC+1, <a href data-email-masked rel="nofollow">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"><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></div></div><div dir="auto"><div dir="auto"><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Mon, Nov 21, 2022, 1:18 AM jing liang <<a rel="noreferrer nofollow">jingli...@gmail.com</a>> wrote:<br></div></div></div></div><div dir="auto"><div dir="auto"><div class="gmail_quote" dir="auto"><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 rel="noreferrer noreferrer nofollow">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" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/7c1fb302-ae85-4a70-88d6-8dca9be6849en%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1669110976089000&usg=AOvVaw0wa-HIwuu-Ez4ZCK7lwqvH">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 rel="noreferrer noreferrer nofollow">cp2k+uns...@googlegroups.com</a>.<br></blockquote></div></div></div><div dir="auto"><div dir="auto"><div class="gmail_quote" dir="auto"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> 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 nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/8c294cd6-a99a-482c-8a84-304cbbbee083n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1669110976089000&usg=AOvVaw2odhJVW3Tp4rkctPg4qQKi">https://groups.google.com/d/msgid/cp2k/8c294cd6-a99a-482c-8a84-304cbbbee083n%40googlegroups.com</a>.<br> </blockquote></div></div></div> </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/af37c62e-90a3-406a-8900-d24b3f31d9b5n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/af37c62e-90a3-406a-8900-d24b3f31d9b5n%40googlegroups.com</a>.<br />