[gmx-users] dynamic cross correlation map

[Yang Ye]

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
>     >
>     >
>     >
>     ------------------------------------------------------------------------
>     >
>     > _______________________________________________
>     > gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     > http://www.gromacs.org/mailman/listinfo/gmx-users
>     > Please search the archive at http://www.gromacs.org/search
>     before posting!
>     > Please don't post (un)subscribe requests to the list. Use the
>     > www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>     --
>     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
>     _______________________________________________
>     gmx-users mailing list     gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> -- 
> 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
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php