[AMBER] filter trajectory with modes same number of frames

From: newamber list <newamberlist.gmail.com>
Date: Sat, 21 Jun 2014 18:07:53 +0100

Hi All

I am trying to filter trajectory along different modes with cpptraj:

trajin traj.nc
rms first :1-312.N
average Avg.rst7 ncrestart
createcrd crd1

reference Avg.rst7.1 [avg]
crdaction crd1 rms ref [avg] :1-382.N
crdaction crd1 matrix covar :1-382.N name NewCovar

runanalysis diagmatrix NewCovar out evecs.dat vecs 936 name test

readdata evecs.dat

crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 8
modes trajout filter_1.nc trajoutfmt netcdf name test pcmin -100 pcmax 100
tmode 1

I have following problems/queries:

1) I always get 201 frames. I am not sure why is it so? No matter how many
frames are there in trajin and which mode I trajout, its always 201.

2) Also how I can get frame number from input trajectory (trajin) which are
filtered out and saved in some output trajectory (modes trajout)

3) Also please let me know if I understood it correctly: If am not wrong
then the filtered trajectory so obtained should contain the extreme
projections? Thus the two extreme projections should 'reflect' the filter
trajectory in summary.

Thanks for any help

AMBER mailing list
Received on Sat Jun 21 2014 - 10:30:02 PDT
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