[gmx-users] dynamic cross correlation map

[Dhananjay]

Thanks you Tsjerk and all,

Yes, the request was for residue correlations. Sorry for not mentioning it
precisely.
I will workout the solutions that were suggested here.

But still, how can I get residue–residue-based correlated motions map ?

Any other way or software ?



-- Dhananjay


On 9/18/07, Yang Ye <leafyoung at yahoo.com> wrote:
>
> g_traj to extract  coordinates, velocities, forces into xvg files for
> you perform calculation.
>
> On 9/18/2007 8:20 PM, Dhananjay wrote:
> > 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
> > <mailto: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
> >     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
> >     <mailto: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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-- 
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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