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Yes, we can agree that they are rigid bodies.<br><br>I would say that you should get equipartitioning of rotational<br>degrees of freedom.<br>g_traj can compute rotational kinetic energies.<br>For you whole system you would have to make each water<br>an index group, select each water in g_traj and add all number up.<br><br>Berk<br><br>> Date: Tue, 15 Sep 2009 12:57:59 +0200<br>> From: alexander.herz@mytum.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] non isotropic kinetic energy<br>> <br>> Berk Hess schrieb:<br>> > Equipartitioning only works per degree of freedom, not per atom.<br>> ><br>> > It works for translation and rotation of a water molecule,<br>> > but that requires a transformation from atomic to COM trans and rot<br>> > coordinates.<br>> <br>> Agreed. As said, we have performed this transfomation using another self<br>> made tool.<br>> Still, after this transformation rotational energy is not equidistributed.<br>> <br>> Can we agree that using constraints or a rigid body approach (so maybe<br>> using quaternions) should<br>> give the same physics (so the same equipartition rules should apply to<br>> both systems)?<br>> Or if we cannot agree on this, what kind of physical objects are<br>> constraint waters if not rigid bodies?<br>> <br>> Alex<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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