Thank you very much for your useful informations sir.
On 16-Feb-2016 9:01 pm, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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.
> > _______________________________________________
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>
>
>
> --
> -------------------------
> 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 Wed Feb 17 2016 - 03:30:03 PST
