[gmx-users] dynamic cross correlation map

[Pedro Alexandre de Araújo Gomes Lapido Loureiro]

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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