[gmx-users] PCA and gmx analyze

[Sun Iba]

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