[gmx-users] calculate the orientation of a group

[David]

On Thu, 2005-07-28 at 16:58 +0200, David Haubertin wrote:
> 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.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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