回复： Re: [gmx-users] Is 2D projection in g_anaeig

[David van der Spoel]

xi zhao wrote:
> Dear sir : Can I understand" 2D projection = Component (PC) Probability 
> Distributions P(v1,v2)"? If this is a true, and how to define the Pmax 
> in detail?
> Thank you in advance! 

you can specify the vectors you want with -v1 -v2

> 
> */Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>/* 写道：
> 
> 
>      > Dear gmx users,
>      >
>      > Does the 2D projection plot has something to do with convergence
>     of the
>      > trajectory? If so, what kind of shape of plot shows the trajectory is
>      > non-converged?
>      >
>      > Normally, I use RMSD plot to see if the trajectory tends to
>     converge. Now
>      > my concern is how to see whether trajectory is conserved or not
>     based on
>      > 2D projection analyses.
>      >
>      > Thanks in advance,
>      >
>      > Linda
>     you can, for example, have a look at the 2D projection of the
>     trajectory
>     onto the first two principal components obtained from the principal
>     component analysis. In this paper Proteins 2005; 60:485 we used this
>     kind
>     of map to check the convergence of the simulation obtained from a
>     replica
>     exchange simulation with the counterpart obtained from high
>     temperature, normal simulation.
> 
>     Phuong
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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