=?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-users]=20Is=202D=20projection?=

[xi zhao]

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! 

Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de> 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
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


 		
---------------------------------
 ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060813/cfc95cdd/attachment.html