[gmx-users] dynamic cross correlation map

[Dhananjay]

Well, I have done 30ns MD simulation for a protein. The protein consists of
4 loop regions.
Using g_cover programme the covariance matrix have been generated and using
g_anaeig programme with option -rmsf , along first 8 eigen vectors the rms
fluction of c-alpha atoms were plotted.
But this is giving me just the information that  particular atom is
fluctuating along particular direction.
I want to know over a 30 ns simulation whether the motions of two atoms or
group of two atoms are correlated or anti correlated. For this I want to
form a dynamics cross correlation map in which I could get the precise
information of group of atoms. The function  used for this kind of analysis
is

C(i,j) = < delta r(i) * delta r(j) > /  sqrt < sqr(delta r(i) ) > . sqrt <
sqr(delta r(j) ) >

the positive C(i,j) -> motions are correlated
the negative C(i,j) -> motions are anti-correlated

I want to plot a 2-D map indicated correlated and anti-correlated motions.

My question is whether it is possible in GROMACS to plot this king of map or
could you please suggest any other free software which could read the
trajectories generated by GROMACS and plot the map.

Again thanking you in advance ......


-- Dhananjay




On 9/18/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Dhananjay wrote:
> > This may be bit different question from main theme.
> >
> > I want to form dynamic cross correlation map as I have trajectories
> > generated by GROMACS 3.3.
> >
> > Please suggest me free software which can read the .trr file for
> > plotting DCCM (dynamic cross correlation map )
> try g_covar or otherwise explain in more detail (equations) what you
> want to do.
>
> >
> > Thanking you in advance....
> >
> >
> >
> > --  Dhananjay
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
Dhananjay C Joshi
Project Assistant
LT & LSB, C D F D
ECIL Road, Nacharam
Hyderabad-500 076, INDIA
Tel : +91-40-27151344
Fax : +91-40-27155610
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