<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Lucas, <div class=""><br class=""></div><div class="">have you conducted the geometry optimization with exactly the same settings, </div><div class="">i.e. basis set, PW cutoff, EPS_SCF, etc.? Since your system has so few DOFs, </div><div class="">fluctuations will be large and conservation by cancellation inherently poor. </div><div class="">Hence, with such a tiny system I would rather stick with NVT instead of NVE + </div><div class="">viral theorem and not use ANGVEL_ZERO … </div><div class=""><br class=""></div><div class="">Greetings, </div><div class="">Thomas</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 21.06.2020 um 07:14 schrieb Lucas Lodeiro <<a href="mailto:eluni...@gmail.com" class="">eluni...@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi all,</div><div class="">I want to perform single molecule molecular dynamics.<br class=""></div><div class="">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 class="">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 class="">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 class="">I attach the files for both MD.</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Has somebody faced these problems? some advice?</div><div class=""><br class=""></div><div class="">regards<br class=""></div><div class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class=""><br class="webkit-block-placeholder"></div>
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