[gmx-users] get 3 roation angles over time

[TJ Piggot]

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 
<tsjerkw at gmail.com> 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,  <marc.spencer at gmx.net> 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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.