I have a little concept problem regarding principal component analysis. So my question is about ED sampling are as follows:
1. I have read from the manual that g_covar calculates and diagonalize the (mass-weighted) covariance matrix. So what is the meaning of mass-weighted in covariance matrix? 2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened the eigenval.xvg file it will shows nothing, i don't know what was wrong with it? 3. what is the difference between covariance matrix and normal mode analysis because both were used to generate the eigenval.xvg and eigenvec.trr file? 4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the structures generated at the time of simulations of single structure without using the other structure? I mean to say that it is possible to use single structure as initial to simulate and ED sampling? 5. what is the need of eigenvec2.trr input file in g_anaeig to generate the single number of covariance matrix as shown in manual? I have used to input only one eigenvec.trr and eigenval.xvg, then it is right to do this? 6. I have used eigenval.xvg as input file in g_anaeig which do not shows nothing when used to open in xmgrace. Then how this file used for generating eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have were successfully generated). 7. One last question is related to g_analyze that it reads ascii file and analyze data sets, but in actual it used some graph.xvg file as input. I am confused about this graph.xvg file which file should I used for input to calculate the cosine content of the principal components. -- Pawan
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