parm WT.prmtop
parm GFP.prmtop
parm MIC.prmtop
parm mCherry.prmtop
trajin WT.mdcrd 1 100 parm WT.prmtop
trajin GFP.mdcrd 1 100 parm  GFP.prmtop
trajin MIC.mdcrd 1 100 parm  MIC.prmtop
trajin mCherry.mdcrd 1 100 parm mCherry.prmtop
reference WT.mdcrd 1 parm WT.prmtop [wt]
reference GFP.mdcrd 1 parm GFP.prmtop [gfp]
reference MIC.mdcrd 1 parm MIC.prmtop [mic]
reference mCherry.mdcrd 1 parm mCherry.prmtop [mch]
rms WT ref [wt] :1-88@C,CA,N,O out rmsd.dat
rms GFP ref [gfp] :1-330@C,CA,N,O out rmsd.dat
rms MIC ref [mic] :1-131@C,CA,N,O out rmsd.dat
rms mCherry ref [mch] :1-345@C,CA,N,O out rmsd.dat

