<div dir="ltr"><div><div><div><div><div><div><div><div><div><div><div>Hi,<br></div><div><br>Yes, you can define the point-plane distance also with respect to the center of mass of some atoms. <br>See <a href="http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/DISTANCE_POINT_PLANE/POINT.html">http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/DISTANCE_POINT_PLANE/POINT.html</a><br><br></div>It should look something like this<br></div><div style="margin-left:40px"><span style="font-family:monospace,monospace">&COLVAR</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">  &DISTANCE_POINT_PLANE</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">    ATOMS_PLANE 2 3 5</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">    ATOM_POINT 1</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">    &POINT</span><br><span style="font-family:monospace,monospace"></span></div></div></div></div></div></div><div style="margin-left:40px"><span style="font-family:monospace,monospace">      TYPE GEO_CENTER<br></span></div><div style="margin-left:40px"><span style="font-family:monospace,monospace">      ATOMS   7 3 1 6                !your phosphate...<br></span></div><div style="margin-left:40px"><span style="font-family:monospace,monospace">    &END POINT</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">  &END DISTANCE_POINT_PLANE</span><br><span style="font-family:monospace,monospace"></span><span style="font-family:monospace,monospace">&END COLVAR</span><br></div></div></div><br></div>Best,<br></div>Ralph<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 20, 2015 at 6:27 AM, TZU-JEN LIN <span dir="ltr"><<a href="mailto:tzujen...@gmail.com" target="_blank">tzujen...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear all CP2K users<br><br>I attempt to do a calculation for pulling phosphate or carbonate out of mineral surfaces by metadynamics.<br>I checked the manual of CP2K, it looks like there is no problem for pulling an ion out of a defined plane, <br>because the collective variable is just the distance between the ion and defined plane.<br>My question is that is it possible to define center of mass of a molecule as a collective variable ? <br>Or I just can only pull phosphorus atom or carbon atoms of phosphate and carbonate respectively out of surface ?<br><br>BEST,<br>Tzu-Jen Lin<span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">

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</font></span></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div><font size="1">Ralph Koitz<br></font></div><font size="1">Binzmühlestrasse 56<br></font></div><font size="1">8050 Zürich<br></font></div><font size="1"><a href="mailto:ralph...@gmail.com" target="_blank">ralph...@gmail.com</a><br>+41 78 600 2093</font><br></div></div></div></div>
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