Hi,
Note that for a large molecule in a relatively small box the rotational
diffusion
is suppressed significantly due to hydrodynamic forces which decay as 1/r.
Berk.
Date: Mon, 7 Jul 2008 18:35:57 -0400
From: [EMAIL PROTECTED]
To: [email protected]; [EMAIL PROTECTED]
Subject: Re: [gmx-users] rot_diff
CC:
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 <[EMAIL PROTECTED]> wrote:
On Sat, 5 Jul 2008 10:40:21 -0400
"rams rams" <[EMAIL PROTECTED]> 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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