<div>Dear Thomas Kühne,</div><div><br></div>thank you for your answer! Is there a way to fold the molecules back after the simulations? I need them to be in the original box since the box was chosen for a specific density of ammonia. I know, for example, GROMACS has an easy way to do this, but I don't know how to make this happen in CP2K.<br><br><div>Best regards,</div><div>Bence Baranyi</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, December 16, 2021 at 11:08:17 AM UTC+1 tkuehne 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;"><div style="word-wrap:break-word;line-break:after-white-space">Dear Bence Baranyi, <div><br></div><div>the coordinates in the output file are not folded back into the simulation box. </div><div>CP2K intern, however, periodic boundary conditions are strictly enforced, so </div><div>your „molecules stay in the initially given cell“. </div><div><br></div><div>Best, </div><div>Thomas Kühne</div><div><div><br><blockquote type="cite"></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space"><div><div><blockquote type="cite"><div>Am 16.12.2021 um 11:01 schrieb Bence Baranyi <<a href data-email-masked rel="nofollow">babu...@gmail.com</a>>:</div><br></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space"><div><div><blockquote type="cite"><div><div>Hi!</div><div>I would like to make a simulation in CP2K, using AM1 on a system containing 33 NH3 molecules, in a cell with 10.855 angstroms as side length and with periodic boundary condition. My aim with this simulation is to get from randomly generated molecule positions to a somewhat realistic arrangement to be used later in an AIMD simulation. How can I ensure that the molecules stay in the said cell during the simulation? I attached the last structure of the simulation (and my input file) and as you can see the max distance between two molecules is clearly bigger than what it could be in a box with 10.855 angstrom sides.</div><div>All help is appreciated!</div><div><br></div></div></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space"><div><div><blockquote type="cite"><div>

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<span><cp2k_am1_33nh3_last.txt></span><span><bulk_33nh3.inp></span></div></blockquote></div></div><br><div>
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