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