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, dresear...@gmail.com 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 href data-email-masked rel="nofollow">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>
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