Hi,
On Mon, May 5, 2014 at 5:23 PM, newamber list <newamberlist.gmail.com> wrote:
> 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?
The plots you refer to are actually histograms generated using the
'hist' command of the principal component projections obtained from
the 'projection' command, see the bottom of the script in
http://pubs.acs.org/doi/suppl/10.1021/ct400862k/suppl_file/ct400862k_si_001.pdf.
> 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
The last 'projection' command will create 3 data sets (corresponding
to projections for PCs 1, 2, and 3) which you can then histogram,
either with cpptraj or your favorite program. It will be probably be
easier to histogram within cpptraj if you name the 'projection' data
sets, e.g.:
crdaction crd1 projection P1 modes evecs.dat out myproj.txt beg 1 end 3 :1-328.N
runanalysis hist P1:1,*,*,*,100 out pca.hist.agr norm name P1-1
etc. See the manual for more details on the 'hist' command (or
alternatively the 'kde' command to use a kernel density estimator
instead).
Hope this helps,
-Dan
>
> Thanks
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 06 2014 - 10:30:04 PDT
