<div>Dear sir:</div> <div>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)?</div> <div>Thank you in advance! <BR><BR><B><I>David van der Spoel <spoel@xray.bmc.uu.se></I></B> 写道：</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">xi zhao wrote:<BR>> Dear sir : Can I understand" 2D projection = Component (PC) Probability <BR>> Distributions P(v1,v2)"? If this is a true, and how to define the Pmax <BR>> in detail?<BR>> Thank you in advance! <BR><BR>you can specify the vectors you want with -v1 -v2<BR><BR>> <BR>> */Nguyen Hoang Phuong <PHUONG@THEOCHEM.UNI-FRANKFURT.DE>/* 写道：<BR>> <BR>> <BR>> > Dear gmx users,<BR>>
><BR>> > Does the 2D projection plot has something to do with convergence<BR>> 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<BR>> converge. Now<BR>> > my concern is how to see whether trajectory is conserved or not<BR>> 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<BR>> 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<BR>> kind<BR>> of map to check the convergence of the simulation obtained from a<BR>> replica<BR>> exchange simulation with the counterpart obtained from high<BR>> 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>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> 雅虎免费邮箱-3.5G容量，20M附件 <HTTP: cn.mail.yahoo.com /><BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> <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><BR><BR>-- <BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept. of Cell and Molecular Biology, Uppsala University.<BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<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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