Thanks a lot, Peng, I use fftw2.1.5 and scampi, it works for single version, and does not work for for paralell. anyway, i will try according to your seggestion. For PCA analysis, first use trjcat -cat file1.trr -file2.trr -o file.xtc -n ca.ndx then use g_cover to analyze the Ca atom or backbone atoms.