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Dear Sir/Madam,<div><br></div><div>I used the following steps to get the cosine content for my trajectories, could you please kindly tell me how to interpret the results?</div><div><br></div><div><div>/usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v</div><div><br></div><div>/usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v eigenvec.trr -proj</div><div><br></div><div>/usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8</div></div><div><br></div><div>In the final "coscont.xvg", I found the followings:</div><div><br></div><div><div><span style="font-size: 10pt; ">+</span><span style="font-size: 10pt; ">+</span><span style="font-size: 10pt; ">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</span></div><div># This file was created Tue Apr 10 10:59:12 2012</div><div># by the following command:</div><div># /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8</div><div>#</div><div># g_analyze_d is p
art of G R O M A C S:</div><div>#</div><div># Giant Rising Ordinary Mutants for A Clerical Setup</div><div>#</div><div>@ title "Cosine content"</div><div>@ xaxis label "set / half periods"</div><div>@ yaxis label "cosine content"</div><div>@TYPE xy</div><div> 1 0.602921</div><div> 2 0.011185</div><div> 3 0.0659901</div><div> 4 0.425943</div><div> 5 0.204306</div><div> 6 0.439315</div><div> 7 0.0288551</div><div> 8 0.0830944</div></div><div>+<span style="font-size: 10pt; ">+</span><span style="font-size: 10pt; ">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</span></div><div><span style="font-size: 10pt; "><br></span></div><div><font size="2">I read some literature quoted the first three PCs's </font>cosine <font size="2">content, if the cosine content close to zero, the trajectory is converged.</font></div><div><span style
="font-size: 10pt; "><br></span></div><div><font size="2">How can I extract the first three PCs's </font>cosine <font size="2">content from the above "conscont.xvg" file? Please kindly help.</font></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; ">Best regards,</span></div><div><span style="font-size: 10pt; "><br></span></div><div><span style="font-size: 10pt; ">Catherine</span></div><div><br></div> </div></body>
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