I am working on membrane protein with residue around 1300. I had completed a 6ns-extended simulation. I am facing a problem in plotting RMSD for protein. I extended my simulation each 1 ns step, so there is six trajectory file which is combined using trjcat.
trjcat -f step1.trr step2.trr step3.trr step4.trr step5.trr step6.trr -o fixed.trr
g_rms command when I am plotting the graph, it is coming something strange which I am attaching below. I am unable to understand the reason of this kind of plot.
Please suggest the problem behind this.