You could use g_principal and follow the change in angles of the three
principal axes of your group using simple maths. This might give you what
you are looking for.
Another way to look at rotations is to use the program DynDom, but this
only works on individual structures not trajectories.
Tom
--On Friday, January 01, 2010 10:49:44 +0100 Tsjerk Wassenaar
<[email protected]> wrote:
Hi Marc,
Which rotation angles? I suppose you mean the Euler angles, but then,
XYZ, XYX, ZYZ? I may be able to help. Contact me off list if you're
interested.
Cheers,
Tsjerk
On Fri, Jan 1, 2010 at 9:02 AM, <[email protected]> wrote:
Dear Gromacs users,
my system consists of two rigid bodies "a" and "b". The body "a" has no
rotation or translation over time. Body "b" rotates and translates over
time. For my system I got the initial structure as PDB file and a XTC
trajectory. How do I get in any easy way from the XTC trajectory the
three rotation angles of the rigid body "b" over time (someting like a 3
column output file) ?
I already searched the gromacs mailinglist and I locked at the commands
"g_rms", "g_rdf", "g_sorient", "g_chi", "g_confrms", "g_bundle" and
"g_rmsf". But it seems that non of the commands really does what I want
:( .
Any help is welcome, thanks and a happy new year
Marc
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Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
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Neuropharmacologist
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TJ Piggot
[email protected]
University of Bristol, UK.
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