[gmx-users] dynamic cross correlation map

[Berk Hess]

What do you need the Maple script for?
Averaging over atoms in groups?

g_covar -xpma gives exactly the cross correlation for each atom pair.

Berk.

>
>I think g_covar -ascii is what you are looking for.
>I have a Maple script that does this kind of graph. If you want you can
>contact me off list.
>
>Regards.
>
>Pedro.
>
>2007/9/18, Dhananjay <dhananjay.c.joshi at gmail.com>:
> >
> > 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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> >


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