Thanks you Tsjerk and all,<br><br>Yes, the request was for residue correlations. Sorry for not mentioning it precisely.<br>I will workout the solutions that were suggested here.<br><br>But still, how can I get residue–residue-based correlated motions map ?
<br><br>Any other way or software ?<br><br><br><br>-- Dhananjay<br><br><br><div><span class="gmail_quote">On 9/18/07, <b class="gmail_sendername">Yang Ye</b> <<a href="mailto:leafyoung@yahoo.com">leafyoung@yahoo.com</a>
> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">g_traj to extract coordinates, velocities, forces into xvg files for<br>you perform calculation.
<br><br>On 9/18/2007 8:20 PM, Dhananjay wrote:<br>> Well, I have done 30ns MD simulation for a protein. The protein<br>> consists of 4 loop regions.<br>> Using g_cover programme the covariance matrix have been generated and
<br>> using g_anaeig programme with option -rmsf , along first 8 eigen<br>> vectors the rms fluction of c-alpha atoms were plotted.<br>> But this is giving me just the information that particular atom is<br>> fluctuating along particular direction.
<br>> I want to know over a 30 ns simulation whether the motions of two<br>> atoms or group of two atoms are correlated or anti correlated. For<br>> this I want to form a dynamics cross correlation map in which I could
<br>> get the precise information of group of atoms. The function used for<br>> this kind of analysis is<br>><br>> C(i,j) = < delta r(i) * delta r(j) > / sqrt < sqr(delta r(i) ) > .<br>> sqrt < sqr(delta r(j) ) >
<br>><br>> the positive C(i,j) -> motions are correlated<br>> the negative C(i,j) -> motions are anti-correlated<br>><br>> I want to plot a 2-D map indicated correlated and anti-correlated<br>> motions.
<br>><br>> My question is whether it is possible in GROMACS to plot this king of<br>> map or could you please suggest any other free software which could<br>> read the trajectories generated by GROMACS and plot the map.
<br>><br>> Again thanking you in advance ......<br>><br>><br>> -- Dhananjay<br>><br>><br>><br>><br>> On 9/18/07, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Dhananjay wrote:<br>> > This may be bit different question from main theme.<br>> >
<br>> > I want to form dynamic cross correlation map as I have trajectories<br>> > generated by GROMACS 3.3.<br>> ><br>> > Please suggest me free software which can read the .trr file for
<br>> > plotting DCCM (dynamic cross correlation map )<br>> try g_covar or otherwise explain in more detail (equations) what you<br>> want to do.<br>><br>> ><br>> > Thanking you in advance....
<br>> ><br>> ><br>> ><br>> > -- Dhananjay<br>> ><br>> ><br>> ><br>> ------------------------------------------------------------------------<br>
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<br>Project Assistant<br>LT & LSB, C D F D<br>ECIL Road, Nacharam<br>Hyderabad-500 076, INDIA<br>Tel : +91-40-27151344<br>Fax : +91-40-27155610