<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 Moon, <div class=""><br class=""></div><div class="">as is customary the coordinates in the output are not folded back into your cell in order to be able </div><div class="">to easily compute transport properties such as the translational diffusion constant via mean squared </div><div class="">displacements. Hence, even though <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">internally periodic boundaries are properly taken into account </span></div><div class="">you may have the sensation that the atoms are spreading out when visualizing them. </div><div class="">If that is case everything everything is fine, but you can fold the coordinates back into the cell when </div><div class="">visualizing them. </div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas Kühne</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 06.12.2022 um 05:10 schrieb Moon Moon <<a href="mailto:yuegrit@gmail.com" class="">yuegrit@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Thank you for your comments.</span><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">The displacement of the atoms is indeed larger and larger, but they don't move to replicas of the box. </div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">I am confused with this phenomenon.<br class=""><br class=""></div><div class="gmail_quote" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div dir="auto" class="gmail_attr">在2022年12月5日星期一 UTC+9 19:01:56<Marcella Iannuzzi> 写道：<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class=""><br class=""></div>?<div class=""><br class=""></div><div class="">By NVT the volume of the simulation cell is constant. </div><div class="">Maybe the displacement of the atoms is larger and larger and you see them moving to replicas of the simulation cell.</div><div class="">Regards</div><div class="">Marcella</div><div class=""><br class=""></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, December 5, 2022 at 5:14:37 AM UTC+1<span class="Apple-converted-space"> </span><a href="" data-email-masked="" rel="nofollow" class="">yue...@gmail.com</a><span class="Apple-converted-space"> </span>wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">hi, could you please help me ?<div class="">When doing MD simulation in NVT ensemble, my simulation box was found become larger and larger. I can't solve this problem.</div><div class="">Attachment are my files. </div><div class="">Any suggestions will be welcomed.</div><div class=""><br class=""></div></blockquote></div></blockquote></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class="webkit-block-placeholder"></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">--<span class="Apple-converted-space"> </span></span><br style="caret-color: rgb(0, 0, 0); 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