Dear Amber users,
I am doing PC analysis using amber14. The script provided below i used for
running the calculation. However, i find the rms square fluctuations of PC1
lesser than that of PC2 and the fluctuation is even larger for PC3 (I mean
the fluctuation is in the following order PC3> PC2>PC1). I checked the
initial rms fitting of crd1 by trajout command and it seems absolutely
fine. I have no clue where i am going wrong. Please suggest me. Thanks in
advance
trajin md.nc
rms first :1-100.CA
average av.nc
createcrd crd1
run
reference av.nc [ref1]
crdaction crd1 rms ref [ref1] :1-100.CA
crdaction crd1 matrix covar :1-100.CA name combinedCovar
runanalysis diagmatrix combinedCovar out evecs.dat vecs 30 name evecs.dat
runanalysis modes fluct name evecs.dat beg 1 end 1 out fluct_1.dat
runanalysis modes fluct name evecs.dat beg 2 end 2 out fluct_2.dat
runanalysis modes fluct name evecs.dat beg 3 end 3 out fluct_3.dat
modes eigenval name evecs.dat out eigenval.dat
--
Rajeswari A,
PhD Research Scholar,
Computational Biophysics Lab,
Department of Biotechnology,
Indian Institute of Technology Madras,
Chennai 600 036, Tamil Nadu, India.
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Received on Mon Feb 15 2016 - 01:30:03 PST
