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