[gmx-users] Re : Re: calculate the orientation of a group

[David Haubertin]

Thanks David,

I thought about editconf, but since I'm dealing with trajectories and
want to monitor orientation vs. time, it won't do.

Still, g_bundle might do the trick if I pick up two groups on each end
of my domain and create a fake helix. I'll give it a go.

David



> > Hi all,
> > 
> > I would like to calculate the orientation of a group in my simulation
> > and cant figure out how to do it.
> > 
> > I have a protein in a membrane, a large part of this protein is in the
> > solvent and has a rigid-body like motion. I'd like to characterise that
> > motion by let's say monitoring the evolution of the principal axis of
> > inertia.
> > 
> > I thought about g_gyrate, but could only retrieve moments of inertia,
> > not the proper axis.
> You can rotate the whole box along the principal moments (using
> editconf) and the rotation matrix should give you the answer. I don't
> think it's printed though
> > 
> > I then thought about g_dipole, but it crashes when I ask for a subgroup..
> > 
> > Any thoughts on that?
> How about g_bundle ?
> 
> 
> > 
> > Thanks in advance
> > 
> > David
> > 
-- 

        David HAUBERTIN            Tel : (+33) 1 69 08 28 63
        Commissariat à l'Energie Atomique -  Centre de Saclay
        Bat. 528 - DSV/DBJC/SBFM - 91191 Gif-sur-Yvette Cedex
        email : dyh at cea.fr