[gmx-users] What is an acceptable cosine content values?

[a a]

Thank  you very much Tsjerk,
I under cosine content much better now.
When you means "that only makes sense for one Pc, the analysis is thus performed per component", could you mind to explain more?
I did the cosine content analysis with the following command " /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8"
So, I got eight rows in my result as follows:
> >  1 0.602921> >  2 0.011185> >  3 0.0659901> >  4 0.425943> >  5 0.204306> >  6 0.439315> >  7 0.0288551> >  8 0.0830944 
Do you mean I should only look at the first row?  
Or should I change the command from eight to one as follows:  " /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 1"
When you said I should perform the analysis per component, do you mean I should also consider row 2-8 above?  If yes, could you teach me how to interpret it too?
Sorry to have so many questions, hope you don't mind.
Best regards & many many thanks in advanced,
Catherine





 
> Date: Thu, 12 Apr 2012 11:53:25 +0200
> Subject: Re: [gmx-users] What is an acceptable cosine content values?
> From: tsjerkw at gmail.com
> To: gmx-users at gromacs.org
> 
> Hi Catherine,
> 
> > When we use cosine content to determine if our simulation are converged or
> > not, should I
> 
> You can't use the cosine content to determine if a simulation is
> converged. You can only use it to determine whether the simulation is
> not converged, which is quite a different thing.
> 
> > (1) sum all the first three principal components together or examine
> > individually?
> 
> Determination of the cosine content is done by means of fitting, and
> the cosine content can be regarded a correlation coefficient, which is
> one for a perfect fit and 0 for no fit. That only makes sense for one
> pc. The analysis is thus performed per component.
> 
> > (2) If I expect the first 10 ns is the equilbrium period, while the other 20
> > ns as the production period.  Should I include all 30 ns of trajectory to
> > the analysis or should I just include the last 20 ns trajectory to the
> > analysis?
> 
> No, you should perform the analysis on the part you intend to use for
> all analysis.
> 
> > (3) Let's if I got the PC1 as low as 0.3, can I still claim the trajectories
> > are converged?
> 
> No. You can claim that the cosine content is low, but that is not the
> same as being converged.
> 
> > (4) Did you comes across that when you increase the simulation time, the
> > cosine content values of the first three principal components did not goes
> > down but increased?
> 
> May very well happen. Especially if the system tips over to a
> previously unexplored region of conformational space due to a
> conformational change or internal rearrangement.
> 
> Cheers,
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> -- 
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