[gmx-users] rot_diff

Xavier Periole X.Periole at rug.nl
Sat Jul 5 18:51:03 CEST 2008

On Sat, 5 Jul 2008 10:40:21 -0400
  "rams rams" <rams.crux at gmail.com> wrote:
> Dear users,
> Is it possible to evaluate the rotational diffusion of proteins using
> gromacs tools ??
No directly. However you can use g_rotacf to generate the autocorrelation
function of vectors (option -d). By defining vectors representing your
molecule/protein you can access the rotational correlation time of your
representative vector. You can imagine different way to get a statistically
significant value. One would be to define many vectors between backbone
atoms and average your results. Another would be to again define many
vectors but this time between the center of mass of the protein and each
Ca atoms and average ...

You can also hack the g_rms code to extract the rotational matrix during
the overlay of your protein to a reference structure and apply it to
a unit vector from whose trajectory you can again use g_rotacf to get
the autocorrelation function of that vector ...

An important point in the comparison of your result to experimental
values is the way the rotational correlation time is extracted
experimentally. They select different mode of relaxation (1 or 2) and thus
you have to use the corresponding Legendre polynomial when calculating the
autocorrelation function. From NMR relaxation l=2.


XAvier Periole - PhD

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

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