[gmx-users] rot_diff
rams rams
rams.crux at gmail.com
Tue Jul 8 00:35:57 CEST 2008
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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