<div> I performed remd using GROMACS 3.3.1 at four different temperatures: 270k, 400k, 540k, 660k, and produced four trajectories. I want to know whether my simulation is ok, but I do not know how to analysis my trajectories. Though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajectory,according to wiki gromacs. In fact, for a REMD simulation, I can not judge whether the simulations is ok , and if they are ok, how to further analyze or extract useful information from trajectories! Are you clear?</div> <div>Thank you for your help! <BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> дµÀ£º</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">xi zhao wrote:<BR>> Dear all users:<BR>> I
performed remd using GROMACS 3.3.1,but I find that I do not know how <BR>> to analyze the result further,<BR><BR>"Analyze" really doesn't tell us what you're trying to do.<BR><BR>> though I have demux.pl script and produced <BR>> replica_index.xvg and replica_temp.xvg files, the contents of two files <BR>> are the same! I use trjcat_d to produce a continuous trajectory,when <BR>> analyzing the trajectory, the system shows segment fault? Please give me <BR>> some advice and analysis tools!<BR><BR>You need to tell us what you're trying to do explicitly. That means text<BR>describing your intentions, a command line that you tried to use, the<BR>output from it, and (potentially) why you think it wasn't what you expected.<BR><BR>A segmentation fault is a generic problem with referencing an illegal<BR>memory location, and thus just about anything could cause it. If there's<BR>no GROMACS-specific error message, though, then it's very likely to be<BR>something
you've done wrongly.<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<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><BR><BR><br><a rel="nofollow" class="plink" target="_blank" href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844 "><img class="pimg" style="" alt="4" src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn" border="0"></a><p> 
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