Well, I have done 30ns MD simulation for a protein. The protein consists of 4 loop regions. <br>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.
<br>But this is giving me just the information that particular atom is fluctuating along particular direction.<br>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
<br><br>C(i,j) = < delta <span style="font-weight: bold;">r</span>(i) * delta <span style="font-weight: bold;">r</span>(j) > / sqrt < sqr(delta <span style="font-weight: bold;">r</span>(i) ) > . sqrt < sqr(delta
<span style="font-weight: bold;">r</span>(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 motions.
<br><br>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.<br><br>Again thanking you in advance ......
<br><br><br>-- Dhananjay<br><br><br><br><br><div><span class="gmail_quote">On 9/18/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">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><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="mailto:spoel@xray.bmc.uu.se">
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