[gmx-users] rot_correlation

Xavier Periole X.Periole at rug.nl
Thu Oct 2 09:09:45 CEST 2008

On Wed, 1 Oct 2008 12:22:03 -0400
  "rams rams" <rams.crux at gmail.com> wrote:
> 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 ??
If I understand correctly you like to generate a duplicate of your
trajectory replacing each frame by a reference structure to remove the
internal motions. You would then use this duplicate trajectory to get
the time auto-correlation function of the NH vectors and extract the
overall rotational correlation time of the protein.
If this is correct it would be equivalent to use the rotation matrix
from g_rms (or any other tool).

Note that if you do not have specific experimental data to compare to it
is not so important which method you use, but you have to explain how you
get the number.
Note also that g_dipole give the molecular dipole relaxation time
which is (I think) what you are looking for.

I hope this helps.
> 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.
> ram.

XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

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