<div>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?</div> <div>Thank you in advance! <BR><BR><B><I>Nguyen Hoang Phuong <phuong@theochem.uni-frankfurt.de></I></B> дµÀ£º</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>> Dear gmx users,<BR>><BR>> Does the 2D projection plot has something to do with convergence of the<BR>> trajectory? If so, what kind of shape of plot shows the trajectory is<BR>> non-converged?<BR>><BR>> Normally, I use RMSD plot to see if the trajectory tends to converge. Now<BR>> my concern is how to see whether trajectory is conserved or not based on<BR>> 2D projection analyses.<BR>><BR>> Thanks in advance,<BR>><BR>> Linda<BR>you can, for example, have a look at the 2D projection of the trajectory <BR>onto the
first two principal components obtained from the principal <BR>component analysis. In this paper Proteins 2005; 60:485 we used this kind <BR>of map to check the convergence of the simulation obtained from a replica <BR>exchange simulation with the counterpart obtained from high temperature, normal simulation.<BR><BR>Phuong<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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