Dear all,
I am using ptraj in order to calculate the time-correlation function
between the principal axis (i.e., the eigenvector associated with the
largest eigenvalue) of two alpha-helices.
Toward this end, I am asking ptraj to print out the principal axis for each
helix. As suggested in the manual, I am not specifying the x or y or z
axis, so that the principal axis will be directly stored in the vector.
vector v0 :645-674.CA principal out v0.out
vector v1 :680-687.CA principal out v1.out
As output, I obtain the following:
# FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
# FORMAT where v? is vector, c? is center of mass...
1 0.7802 -0.6004 -0.1756 91.2485 76.1624 37.2220 92.0287 75.5620
37.0464
2 0.8411 -0.5380 -0.0568 91.2706 75.7294 30.84117.1629 92.1117
75.1914 37.1061
3 0.6899 0.5752 0.4396 91.1414 36.6761 91.7030 76.7166 37.1157
I assume that the principal axis is stored in the second column (0.7802,
0.8411, 0.6899 ...).
Could you please clarify this point?
Moreover, if I subsequently specify the following command in order to
obtain the time-correlation between v0 and v1, I do not obtain any output.
analyze timecorr vec1 v0 vec2 v1 tstep 1.0 tcorr 10000.0 out v0_v1.out
Do you have any suggestions that can help me in doing this analysis?
Thank you
Best regards
Giulia
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Received on Wed Nov 12 2014 - 10:30:02 PST
