<div dir="ltr"><div class="gmail_quote">On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin <span dir="ltr"><<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font size="3" face="arial, helvetica, sans-serif"><span style="font-size: 12px; white-space: pre-wrap;"></span></font><div><span style="font-family: arial,helvetica,sans-serif; font-size: 12px; white-space: pre-wrap;">
So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ?</span><br></div></blockquote></div><br>Removing PBC and placing atoms back into their "true" location is easy. In general, if an atom has moved more than half of the box between two consecutive timesteps then it has "jumped" over the box.<br>
You can see for example eq. 19 & 20 in doi:10.1063/1.2968608 .<br>--Omer.<br></div>