Hi everyone. Nowadays I am learning how to analyze my results after MD. I have been reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and all is fine but I have a big doubt about g_rms. I know that g_rms compares two structures by computing the root mean square deviation (RMSD). In the tutorial one part said:
"Use g_rms to obtain an RMSD plot of the protein backbone and the drug (IN4) throughout the simulation. Do the Backbone first g_rms –s md.tpr –f md.trr (or xtc) –o bkbone_rmsd.xvg You will be prompted to select a Group. Enter 4 (for backbone). Compare to 1 Group in the reference. Enter 1 then Enter 4 for backbone again." The last part for me is confused, I understand that I am going to compare backbone with protein so first (4) and then (1), but "Enter 1 then Enter 4 for backbone again", why???? and what should I do if I want to calculate the RMSD of the drug? (4) and then LIG?? or (LIG) and (LIG)? I know that these are trivial questions but I would be grateful I someone can help me or give advices. Thanks in advance. Miguel.
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