
#ptraj GAAC-ions.topo

trajin GAAC3-strip.crd 1 9999999 1

reference parmindex 0 /uufs/chpc.utah.edu/common/home/u0181375/dirs/cheatham-group2/cheatham/GAAC/anton-abc/GAAC/avgpdb/avg_0-10us-ions.pdb
rms reference mass :5-14,23-32 out tmprms.dat time 50

strip :1-4,15-22,33-99999
strip @H=
strip @?H=

rmsavgcorr mass out rmscorr-internal-strip4n.dat \
  reference avg0.pdb \
  * "!(:1-4,15-22,33-999999 | @H=)" \
  stop 200000 offset 50

datafile rmscorr-internal-strip4n.dat time 2500
