Hi all, (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory and one mutant trajectory using the following command:
g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n wt_backbone.ndx The file wt_backbone.ndx contains the backbone of the protein (Backbone indices are identical between wt and mutant). The result is that I am getting a well deserved error saying that wt.xtc and mutant.xtc has different number of atoms (the tpr itself): Fatal error: Second trajectory (76128 atoms) does not match the first one (76129 atoms) So the question becomes: Is there a (convenient) way to produce rms-matrix between wt and mutant? Or perhaps circumvent this problem in some other way? I tried looking into g_confrms, but apparently it works only on two frames instead of trajectories. Thanks a lot, -Shay
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