Dear all, I'm running my first simulation of a dimer. When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get the RMSD of the whole dimer, the graph is ascending, till reaching a value of 8 A. in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole dimer.
However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one chain (one monomer), the graph is constant with value around 1 A. and this for both chains, when taken alone. In this case, I take a .tpr file, a .xtc file and a .ndx file of the monomer. So is this an error of using g_rms? Thank you. Carla
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