
#ptraj GAAC-ions.topo

trajin GAAC3-strip.crd

#parm GAAC-nowater.topo
reference parmindex 0 /uufs/chpc.utah.edu/common/home/u0181375/dirs/biodata8/cheatham/anton-abc/GAAC/avgpdb/avg_0-10us-ions.pdb
rms reference mass :3-16,21-34

strip :35-99999
strip @H=
strip @?H=
strip :17-20
strip :1-2

rmsavgcorr mass out rmscorr-fit-strip.dat stop 200000
datafile rmscorr-fit-strip.dat time 50
