Hi,
On Mon, Feb 15, 2016 at 2:02 AM, Rajeswari A.
<rajeswari.biotech.gmail.com> wrote:
> 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
OK, I'm pretty sure I know what's happening here. When the 'modes'
analysis code was originally written in ptraj it was assumed that your
eigenvalues have been converted to frequencies, which is what happens
automatically when you use a mass-weighted covariance matrix. I've
been meaning to make the code smarter about realizing if this has been
done or not in cpptraj but haven't gotten to it yet. I recommend
repeating the calculation using a mass-weighted covariance matrix
(mwcovar).
Thanks for the report,
-Dan
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Feb 16 2016 - 08:00:03 PST
