[gmx-users] rot_diff

Xavier Periole X.Periole at rug.nl
Tue Jul 8 09:31:10 CEST 2008

Have a look at those papers.

On Mon, 7 Jul 2008 18:35:57 -0400
  "rams rams" <rams.crux at gmail.com> wrote:
> Dear XAvier,
> Thanks for your reply and for the explanation. I am not an NMR guy so I
> would like to know little bit of more about the way we can calculate the
> rotational diffusion. The way I understood is the following and let me know
> if I am wrong.
> After obtaining the rotaional correlation function using Gromacs tools
> (g_rotacf), I need to calculate the correlation time I suppose.
> The obtained correlation time is related with the local diffusion constant
> (d) by the relation
> d = 1/l(l+1) t
> t is the correlation time obtained above and l = 1 or 2 depends upon the
> order of the legendre polynomial we will use in the g_rotacf and the
> experimental results with which we are comparing.
> then by solving the following relation
> d=n'Qn (n is a unit vector lies along the vector connecting the two spins),
> we can obtain "Q" which inturn is in relation with D (the diffusion tensor).
> Thats the overall idea I have but I am sure I need to worry alot of finer
> other details while I start putting my hands into it. If the overall idea is
> alright I could put the things in a more detailed way.
> Ram.
> On Sat, Jul 5, 2008 at 12:51 PM, Xavier Periole <X.Periole at rug.nl> wrote:
>> 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.
>> -----------------------------------------------------
>> XAvier Periole - PhD
>> Molecular Dynamics Group
>> - NMR and Computation -
>> University of Groningen
>> The Netherlands
>> -----------------------------------------------------
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XAvier Periole - PhD

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

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