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 <[EMAIL PROTECTED]>/* 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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