<div dir="ltr"><div>Dear Matthew:</div><div>good afternoon.</div><div>Sorry to bother once more.</div><div>I took Gly and Ala oriented the way that their COO-Ca-N plane is parallel to XZ plane</div><div>and modeled charge dynamics propagating under such 5 field settings <br></div><div>{Ex = 0, Ey = 0} no field<br></div><div>{Ex=0, Ey} polarized along Y<br></div><div>{Ex, Ey = 0} polarized along X<br></div><div>{Ex, Ey + P/2 shifted} left circular polarized<br></div><div> {Ex, Ey - P/2 shifted} right circular polarized.</div><div><br></div><div>The initial geometries are proximal to the global minimum optimized under DFT.</div><div></div><div><br></div><div>I attach an image where I sum-up the results.</div><div>When there are no fields, apparently, there is just the equillibration: energy flows into kinetic populating vibrations,</div><div>and there is the intra-molecular H dynamics between the terminals.</div><div><br> </div><div>Field polarized along X (parallel to the COO-Ca-N plane ) makes thermalization slowe.</div><div><br></div><div>Field polarized along Y (perpendicular to the COO-Ca-N plane) introduce strong anticorrelation of side groups charges for Gly,</div><div>but it does not slow down the thermalization for Gly.</div><div>Instead, in the case of Ala, the temperature and the kinetic energy explode at a certain point - the shake up start to break the molecule.</div><div>At the same time, the shake up for the potential energy is about the same as when field is parallel to X.</div><div></div><div>This is peculiar since one could think that shaking between the terminals should have larger effect. <br></div><div><br></div><div>Using CD polarized light, phase of charge modulations of the side groups, only, reflect "chirality" of the drive.</div><div>In the case of Ala, cp2k simulates both, the temperature and the kinetic energy explode at a certain point.</div><div><br></div><div>I simulate using energy constraining NVE and instructing T=300K.<br></div><div>Potential energy does change smooth, always.</div><div><br></div><div>I wish to ask your opinion: the increase of temperature as cp2k simulate is it a signature</div><div>of investing energy into molecule that it start to break it apart "properly",</div><div>or it is a "proper" mis-performance of the NVE part of the equations,</div><div>or it is a signature of the equations collapse?</div><div><br></div><div>I doubt about the third because I tested increasing the amplitude of the drive: at certain point</div><div>the potential energy start to show a ripple.</div><div>The data I attach here does show potential energy to vary smoothly.</div><div></div><div><br></div><div>Therefore, I think it is likely that the molecule is getting very hot.</div><div><br></div><div>Thank you.</div><div><br></div><div>With best,</div><div></div><div>Victor <br></div><div> <br></div><div><br></div><div><br></div><div> <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 22, 2023 at 4:56 PM Matt Watkins <<a href="mailto:mattwatkinsuk@gmail.com">mattwatkinsuk@gmail.com</a>> wrote:<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>Hi Victor,</div><div>from your setup the main things are:</div><div><ul><li>the cutoff is too small - should be set like a standard DFT calculation - something around 400 Ry and the REL_CUTOFF to 60 Ry or similar.</li><li>the timestep is very aggressive. If you plot your energy as function of time I think you will see the conserved quantity drift badly at some point in your simulation and then it explodes. Try something like <br><ul><li><span style="font-family:Courier New">stepsize [au_t] 0.1</span></li></ul></li></ul></div><div>Matt<br></div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, 19 May 2023 at 07:48:32 UTC+1 Victor Volkov wrote:<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></div><div>Good day.<br></div><div>I am exploring molecular dynamics under field.</div><div></div><div></div><div>I set glycine at the center of a box,</div><div>and suggested Ehrenfest dynamics with a time step of about 0.04 fs,</div><div>while the custom field file sets the external field to ZERO. <br></div><div></div><div></div><div>The simulation proceeds alright, till the time-frame 500, after which</div><div>there is a peculiar structural "expansion".</div><div></div><div><b>Q1: Would you comment this?</b></div><div></div><div>Also, I attach a fragment of the momentum file:</div><div>CP2K prints reference point position to be "chaotic",</div><div>while I select REFERENCE COAC: since the atomic charges of the glycine, <br></div><div>the reference point should be next to the C-alpha atom. <br></div><div></div><div> <b>Q2: would you comment on the usage of the setting I selected? </b><b><br></b></div><div></div><div>Thank you.</div><div>Victor<br> </div><div><br></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" 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/c389ccfe-3201-4f0a-83e7-e931000e2366n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/c389ccfe-3201-4f0a-83e7-e931000e2366n%40googlegroups.com</a>.<br> </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/CAK%2B-SShB7Zus2w2LJs8xSQxns2fRpzcTqTVp8pHJdHcWOC8D2Q%40mail.gmail.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/CAK%2B-SShB7Zus2w2LJs8xSQxns2fRpzcTqTVp8pHJdHcWOC8D2Q%40mail.gmail.com</a>.<br />