parm  complex_solv.prmtop
trajin trajout10-51.mdcrd
strip !(:1-273&!@H=)
rms mass first :1-273&!@H=
average crdset ex_average
createcrd ex_trajectories
run
crdaction ALL-trajectories rms ref ALL-average :1-273&!@H=
crdaction ALL-trajectories matrix covar name ALL-covar :1-273&!@H=
runanalysis diagmatrix ALL-covar out ALL-evecs.dat vecs 3 name ALLEvecs nmwiz nmwizvecs 3 nmwizfile ALL.nmd nmwizmask :1-273&!@H=
crdaction ALL-trajectories projection WTP1 modes ALLEvecs beg 1 end 3 :1-273&!@H= crdframes 1,84000
hist ex1:1 bins 100 out 5drb_hist.agr norm name ex1-1
hist ex1:2 bins 100 out 5drb_hist.agr norm name ex1-2
hist ex1:3 bins 100 out 5drb_hist.agr norm name ex1-3
runanalysis
clear all
readdata ALL-evecs.dat name ALLEvecs
parm complex_solv.prmtop
parmstrip !(:1-273&!@H=)
parmwrite out ALL-modes.prmtop
runanalysis modes name ALLEvecs trajout ALL-mode1.crd pcmin -100 pcmax 100 tmode 1 trajoutmask :1-273&!@H= trajoutfmt crd
runanalysis modes name ALLEvecs trajout ALL-mode2.crd pcmin -100 pcmax 100 tmode 2 trajoutmask :1-273&!@H= trajoutfmt crd
runanalysis modes name ALLEvecs trajout ALL-mode3.crd pcmin -100 pcmax 100 tmode 3 trajoutmask :1-273&!@H= trajoutfmt crd
go
quit
