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
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