[gmx-users] dynamic cross correlation map

Tue Sep 18 16:50:08 CEST 2007

Hi,

g_covar -h says that -xpma gives the cross-covariance, not the correlation...
Also, I believe the request was for residue correlations, although not
specified in what way. Anyway, at present g_covar does not give
correlations, but that is easy enough. g_covar -ascii gives a raw
covariance matrix, of which the sqrt of the diagonal elements can be
used to obtain the correlations, but that won't yet give the residue
correlations.

Tsjerk

On 9/18/07, Berk Hess <gmx3 at hotmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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