<div dir="ltr"><div>Thanks Thomas for the advice about the MD.</div><div><br></div><div>Yes the geometry optimization was with the same settings, using the default convergence criteria. I attach the input and output.</div><div>There is a little energy difference (1 E-5) between the geo_opt run (optimized configuration) and the zero step in the MD, due to the centering positions keyword, I understand that is due to non-<span lang="en"><span title="">continuous </span></span>fourier grid. But the potential energy minima along the MD is 1 E-4 lower than the geo_opt geometry minima... and I cannot understand why.</div><div><br></div><div>Regards</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 22 jun. 2020 a las 5:54, Thomas Kühne (<<a href="mailto:tku...@gmail.com">tku...@gmail.com</a>>) escribió:<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 style="overflow-wrap: break-word;">Dear Lucas, <div><br></div><div>have you conducted the geometry optimization with exactly the same settings, </div><div>i.e. basis set, PW cutoff, EPS_SCF, etc.? Since your system has so few DOFs, </div><div>fluctuations will be large and conservation by cancellation inherently poor. </div><div>Hence, with such a tiny system I would rather stick with NVT instead of NVE + </div><div>viral theorem and not use ANGVEL_ZERO … </div><div><br></div><div>Greetings, </div><div>Thomas</div><div><div><br><blockquote type="cite"><div>Am 21.06.2020 um 07:14 schrieb Lucas Lodeiro <<a href="mailto:eluni...@gmail.com" target="_blank">eluni...@gmail.com</a>>:</div><br><div><div dir="ltr"><div>Hi all,</div><div>I want to perform single molecule molecular dynamics.<br></div><div>First I do a convergence test for cutoff, cell size and poisson solver. I read in old mails, that MT is better than WAVELET for MD, due to the first is translational invariant.</div><div>After that I start a MD from the optimized molecular geometry at the same level of theory. I want to obtain statistical information for a given temperature (300K for example), I think an NVT is not well behaved for a single molecule, then I ran NVE MD. As the geometry is at the minimum, I start with 2*T (where T is the target temperature) thinking in virial theorem (at equilibrium equal potential and kinetic energy).</div><div>But the system is not converging (the average temperature) at the desired temperature. It shows a weird temperature oscillation (different as expected due to bond oscillation), it present in some moment higher temperature than the initial and a potential energy lower than the initial... Also, the molecular rotation exhibits variations along the MD and translation in the box. For that I start a new MD with the same INPUT and geometry, adding ANGVEL_ZERO. The MD starts without rotation but in 300 fs it starts to rotate.</div><div>I attach the files for both MD.</div><div><br></div><div>I read about the geometrical constraints, it would be useful for diatomic molecules, but for H2O or complexer molecules is not a solution.</div><div><br></div><div>Has somebody faced these problems? some advice?</div><div><br></div><div>regards<br></div><div></div><div><br></div><div><br></div></div><div><br></div>
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