[gmx-users] rot_correlation

rams rams rams.crux at gmail.com
Wed Oct 1 18:22:03 CEST 2008

Hi Xavier,

I started working on the g_rms program (to obtain the rotation matrices)
suggested by you as well as it was mentioned in a couple of papers for the
calcualtion of rotational correlation times of proteins.

Meanwhile, I have an idea like the following :

The problem in using the MD generated trajectory to obtain the rotational
correlation times is, the vectors / the system will have all the three
degrees of freedom here. (Though by using the option -fit rot+trans option
in trjconv, we can remove the translational and rotational degrees of
freedom but still the internal vibrations are there). Where as for obtaining
the rotational correaltion times, we like to know how a particular vector or
a system is reorienting during the course of the simulation alone.

For this, if I superimpose my reference structure (.tpr) on the structures
generated at different time scales (it is just opposite to the regular rms
fits) and if I generate a trajectory with the rotated structures of .tpr
files at various time intervals, this trajectory gives me the orientation of
a vector / system at different time scales. Also the lenghts of the vectors
are also the same (hence no need to worry about the internal motions). Can I
use this trajectory to obtain the rotaitonal correlation times ??

Though its lot of work to do the things manually, but i can give a try if it
is alright to try in the above mentioned way.

Thanks in advance.

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