=?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-use?= =?gb2312?q?rs]=20Is=202D=20projection=20in=20g=5Fanaeig?=

[xi zhao]

Dear sir:
  I am sorry. Can  I understand" 2D projection = Probability Distributions P(v1,v2) in Proteins 2005; 60:485. How to produce 3D plot of P(v1,v2)? how can I look for transit paths from  P(v1,v2)? How can I calculate free enery in gromacs using P(v1,v2)?
  Thank you in advance! 

David van der Spoel <spoel at xray.bmc.uu.se> дµÀ£º
  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 
/* дµÀ£º
> 
> 
> > 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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