parm ../ADP/compl_dry.prmtop [ADP] 
parm ../inhibitor_002/compl_dry.prmtop [inh]
trajin ../ADP/prod1/p1_90.mdcrd parm [ADP]
trajin ../ADP/prod2/p2_90.mdcrd parm [ADP]
trajin ../ADP/prod3/p3_90.mdcrd parm [ADP]
trajin ../inhibitor_002/prod1/p1_90.mdcrd parm [inh] 
trajin ../inhibitor_002/prod2/p2_90.mdcrd parm [inh]
trajin ../inhibitor_002/prod3/p3_90.mdcrd parm [inh]
rms mass first :1-316@CA,C,N,O,H
average crdset ALL-average :1-316@CA,C,N,O,H start 1 stop 54000
createcrd ALL-trajectories
run
crdaction ALL-trajectories rms ref ALL-average :1-316@CA,C,N,O,H
crdaction ALL-trajectories matrix covar name ALL-covar :1-316@CA,C,N,O,H
runanalysis diagmatrix ALL-covar out ALL-evecs.dat vecs 3 name ALLEvecs nmwiz nmwizvecs 3 nmwizfile ALL.nmd nmwizmask :1-316@CA,C,N,O,H
crdaction ALL-trajectories projection ADP1 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 1,9000
crdaction ALL-trajectories projection ADP2 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 9001,18000
crdaction ALL-trajectories projection ADP3 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 18001,27000
crdaction ALL-trajectories projection inh1 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 27001,36000
crdaction ALL-trajectories projection inh2 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 36001,45000
crdaction ALL-trajectories projection inh3 modes ALLEvecs beg 1 end 3 :1-316@CA,C,N,O,H crdframes 45001,54000
hist ADP1:1 bins 100 out ADP-hist.agr norm name ADP1-1
hist ADP1:2 bins 100 out ADP-hist.agr norm name ADP1-2
hist ADP1:3 bins 100 out ADP-hist.agr norm name ADP1-3
hist ADP2:1 bins 100 out ADP-hist.agr norm name ADP2-1
hist ADP2:2 bins 100 out ADP-hist.agr norm name ADP2-2
hist ADP2:3 bins 100 out ADP-hist.agr norm name ADP2-3
hist ADP3:1 bins 100 out ADP-hist.agr norm name ADP3-1
hist ADP3:2 bins 100 out ADP-hist.agr norm name ADP3-2
hist ADP3:3 bins 100 out ADP-hist.agr norm name ADP3-3
hist inh1:1 bins 100 out ADP-hist.agr norm name inh1-1
hist inh1:2 bins 100 out ADP-hist.agr norm name inh1-2
hist inh1:3 bins 100 out ADP-hist.agr norm name inh1-3
hist inh2:1 bins 100 out ADP-hist.agr norm name inh2-1
hist inh2:2 bins 100 out ADP-hist.agr norm name inh2-2
hist inh2:3 bins 100 out ADP-hist.agr norm name inh2-3
hist inh3:1 bins 100 out ADP-hist.agr norm name inh3-1
hist inh3:2 bins 100 out ADP-hist.agr norm name inh3-2
hist inh3:3 bins 100 out ADP-hist.agr norm name inh3-3
run
clear all
readdata ALL-evecs.dat name ALLEvecs
parm ../ADP/compl_dry.prmtop
parmstrip !(:1-316@CA,C,N,O,H)
parmwrite out ALL-modes.prmtop
runanalysis modes name ALLEvecs trajout ALL-mode1.nc pcmin -100 pcmax 100 tmode 1 trajoutmask :1-316@CA,C,N,O,H trajoutfmt netcdf
runanalysis modes name ALLEvecs trajout ALL-mode2.nc pcmin -100 pcmax 100 tmode 2 trajoutmask :1-316@CA,C,N,O,H trajoutfmt netcdf
runanalysis modes name ALLEvecs trajout ALL-mode3.nc pcmin -100 pcmax 100 tmode 3 trajoutmask :1-316@CA,C,N,O,H trajoutfmt netcdf
