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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: > > > > > > 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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > > > > > 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. > > > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > > > _______________________________________________ > > > > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] . > > > > 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@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 [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > >_______________________________________________ > >gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > >Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Play online games with your friends with Messenger > http://www.join.msn.com/messenger/overview > > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php