Dear All, Before and after extention we have 2 trajectorty files, and by trjcat we got we, then we can do the g_rms g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns But here for the g_rms command I find no matter whether we use the *.tpr of the initiation of the production MD, or the *.tpr for the initiation of the extension part, the rmsd.xvg curves seems same. Will you please give some comment on it? Cheers, Acoot
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