[gmx-users] PCA and gmx analyze

[sun]

Allright Sir.
Thank you very much

Sent from my iPhone

> On 27-Jun-2016, at 4:55 pm, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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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