[gmx-users] dynamic cross correlation map
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 18 20:31:26 CEST 2007
Dhananjay wrote:
> 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 ?
It's matter of how you define it. An easy way would be to try C-alphas.
>
> Any other way or software ?
>
>
>
> -- Dhananjay
>
>
> On 9/18/07, *Yang Ye* <leafyoung at yahoo.com <mailto: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>
> > <mailto: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>
> > <mailto: spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> spoel at gromacs.org
> <mailto:spoel at gromacs.org>
> > <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
> http://folding.bmc.uu.se <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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>
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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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