Dear all,
I performed essential dynamics analysis on two proteins at
different temperatures ranging from 300 K to 473 K; subsequently I tried to
calculate RMSIP (root mean square inner product) to determine the subspace
overlap between two different trajectories at different temperatures. For
reference values, I have divided each trajectory in two halves and have
calculated the RMSIP between the first 10 essential eigenvectors of each half.
At lower temperature I am getting values like 0.71-0.75, but at higher
temperature it is like 0.58-0.6. My questions are
1) At lower temperature I considered equilibrated part of trajectories to
calculate RMSIP, but at higher temperature I can not get equilibrated
trajectory, as the fluctuations are too high, so in that case is it necessary
to calculate RMSIP, or better to say how much we can rely upon RMSIP value to
interpret the overlap between two different trajectories.
2) Some authors plotted RMSIP over time (Ref J Mol Graph Model. 2008 26,
1091-103) The overlap.xvg file produces subspace overlap values of the
eigenvectors in the file -v2 with eigenvectors –first to –last in the file –v.
But I could not generate RMSIP over time plot, Is it necessary to divide the
trajectory in several subparts and then calculate RMSIP between them over time,
or is there any option in Gromacs that can plot directly RMSIP over time?
3) I have another question regarding g_covar and g_anaeig, eigenval.xvg
produces eigenvalues over eigenvector index, and –rmsf option of g_anaeig
produces rmsf fluctuation per atom of eigenvectors –first –last, but several
authors represent total fluctuation vs eigenvector index and from it predict
the individual contribution of eigenvectors. Does it mean that I have to
consider cumulative fluctuation of the atoms in eigrmsf.xvg file and plot them
against eigenvector index, I am not very sure that if it is correct or not,
please suggest how to generate this kind of plot, Thanks in advance........
Regards
Sangeeta
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