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 > ----------------------------------------------------- > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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