[gmx-users] PCA and gmx analyze

[Tsjerk Wassenaar]

Hi Suniba,

Don't look at the cosine content. It doesn't convey anything useful. If you
want to know more, I've posted more lengthy remarks about it before.

Cheers,

Tsjerk
On Jun 27, 2016 1:11 PM, "Sun Iba" <sun.iba2 at gmail.com> wrote:

> Hello Users and experts
>
> My system details:
> Force field: GROMOS 43a1
>
> Gromacs version: 5.0
>
> OS: Ubuntu 14.0
>
> Simulation time: 200 ns
>
> No. of eigenvectors and eigenvalues in gmx covar and gmx anaeig: 378
> Protein backbone was used for least square fit and covariance analysis. I
> am trying to monitor protein folding in the presence of a small molecule
> and interested in using first 2 PCs for FEL. Also, I am interested in
> assessing if the system is not converged. When I tried to analyze the
> cosine content of my eigenvectors with gmx analyze i get following results:
>
> Command line:
>   gmx analyze -f proj.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -av
> average.xvg -ee errest.xvg -b 100000 -e 150000
>
> Read 1 sets of 5001 points, dt = 10
>
>                                                  std.
> dev.                      relative deviation of
>                               standard        ---------
>     cumulants from those of
> set      average         deviation      sqrt(n-1)                      a
> Gaussian distribition
>
> cum. 3   cum. 4
> SS1  -2.974823e+00   1.492213e-01   2.110308e-03       0.381    0.401
>
>
>
> 2500, time=25000
>
>
> *Cosine content of set 1 with 0.5 periods: 1.14745e-05*
>
>
>
> Set   1:  err.est. 0.0155418  a 0.693315  tau1 12.3624  tau2 856.505
>
> Back Off! I just backed up autocorr.xvg to ./#autocorr.xvg.1#
>
> Can anyone help me with cosine content of set 1? I dont understand it.
> According to manual the cosine content should be closer to 1. Is that value
> (* 1.14745e-05) *considered to be closer to 1?
> .
>
> Thank You
> Suniba
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