[gmx-users] query about essential dynamics

sangeeta kundu sangeeta0983 at yahoo.co.in
Fri Aug 1 12:58:03 CEST 2008

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........

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