Dear All
I am doing PCA for my polymer using similar commands taken from (recently
suggested by Daniel):
http://pubs.acs.org/doi/suppl/10.1021/ct400862k/suppl_file/ct400862k_si_001.pdf
I have following two queries:
1) I want to do it for my whole simulation for 100ns saved in parts but
each traj is about 1.5GB so cpptraj gets killed in between. I can use
stripped traj and make stripped prmtop with PARMED but is it possible to
strip prmtop within cpptraj and plug it further for analysis. Like this
(though it does not work because new stripped traj would expect new prmtop)
trajin 1.trj.nc
strip !(1-328.N)
trajin 2.traj.nc
srtip !(1-328.N)
2) Also in many papers there are Principal component plots. If am not
wrong these are same obtained from 'projection modes' as shown below
(myproj.txt). Or its something else?
(just a test for two trajectories and I should get both trajectories frames
stored in crd1 but, as expected, it does not work if I have 100 such traj)
trajin 1trj.nc
trajin 2trj.nc
rms first :1-328.N
average Avg.rst7 ncrestart
createcrd crd1
run
reference Avg.rst7.1 [avg]
crdaction crd1 rms ref [avg] :1-328.N
crdaction crd1 matrix covar :1-328.N name myCovar
runanalysis diagmatrix myCovar out evecs.dat vecs 15
readdata evecs.dat
crdaction crd1 projection modes evecs.dat out myproj.txt beg 1 end 3
:1-328.N
Thanks
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Received on Mon May 05 2014 - 16:30:03 PDT
