<div dir="ltr"><div>Dear Matthew:</div><div>good afternoon.</div><div>Thank you for the kind reply.</div><div><br></div><div>Indeed, the cut-of is too small. <br></div><div>Thank you.</div><div><br></div><div>>
the timestep is very aggressive. <br></div><div><br></div><div>This is curious.</div><div>I always thought that under-sampling (using a longer time-step to speed up simulated results)</div><div>is a problem.</div><div>I selected the time-step to over-sample (a bit) a period which would correspond</div><div>to oscillation of a field in near UV - about 230 nm.</div><div>Oversampling would be necessary to model circular polarized perturbation using two fields,<br></div><div>when the second one (0 1 0) is Pi/2 shifted in respect to the first (1 0 0), if "propagation"</div><div>is considered along Z (0 0 1).</div><div>In principle, I am curious to see two things: <br></div><div>1) if the external field could be such that molecule would break apart;</div><div>2) if, then what kind of fragments and how they would fly away according to the driving conditions.</div><div><br></div><div>It is a sort sense if a "destruction of the Hamiltonian" may mimic certain event upon ionisation,</div><div>not all events but some.</div><div><br></div><div>Thank you again.</div><div>With best regards.<br></div><div>Victor<br></div><div><br></div><div>.</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>
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