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Created June 30, 2015 02:32
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gistfile1.txt
trajin ../../prod_1.nc 1 2500 5 # 10ns each
... (place holder) ..
trajin ../../prod_100.nc 1 2500 5
rms reference ../../build/system/060315.prmtop :38-328@CA,C,N
# PCA analysis for phosphoserine 335
matrix covar name PCA :335&!@H=
analyze matrix PCA vecs 25 out evec.pev
go
projection :335&!@H= modes evec.pev out proj.ppj beg 1 end 3
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