Thanks a lot for the reply.<div>But I am getting different results with the two .tpr files (first and last) using the following commands:</div><div><br></div><div>trjconv -s <b>first.tpr </b>-f test.xtc -o str.gro -dump 10000 -pbc nojump</div>
<div>trjconv -s <b>last.tpr</b> -f test.xtc -o str.gro -dump 10000 -pbc nojump</div><div><br></div><div>So which .tpr file should I use?</div><div><br></div><div>Thanks,</div><div><br></div><div>Anirban</div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div>
<br><div class="gmail_quote">On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On 4/12/2010 4:33 PM, Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks a lot for the reply.<br>
Actually I am running a protein in lipid bilayer. Now I want to<br>
calculate the thickness of the bilayer at the end of the simulation.<br>
So for that I want the last structure (.gro) file. So I am trying to<br>
dump the last structure using trjconv (with -pbc option). So to do<br>
this which .tpr file should I supply to trjconv, the first one or the<br>
last one?<br>
</blockquote>
<br></div>
Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks again.<br>
<br>
Anirban<br>
<br>
On 12/4/10, Justin A. Lemkul<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks a lot Justin for the reply. Yes, I understand that. But ideally<br>
which structure should be used as the reference, in a general, the<br>
starting structure or the end structure?<br>
</blockquote>
That's up to you to decide based on what you need to measure. Do you want<br>
the<br>
RMSD relative to your starting (i.e. crystal/NMR) structure, or are you<br>
trying<br>
to study how a protein folds, in which case you'd use the native (end)<br>
state?<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
like when I an using trjconv to dump my last frame (with "-pbc nojump"),<br>
which .tpr file should I use to get the exact picture of what has<br>
happened to my protein at the end of the simulation. Should I use the<br>
first .tpr file or the last .tpr file?<br>
<br>
</blockquote>
I don't understand what you mean. "What has happened" is an entire<br>
trajectory,<br>
not a snapshot.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks a lot again.<br>
<br>
Anirban<br>
<br>
On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Anirban Ghosh wrote:<br>
<br>
Hi ALL,<br>
<br>
Its a very basic question but still...<br>
When we calculate RMSD (or any other parameter) using the g_rms<br>
command, we need to supply the .tpr file with -s option. Now<br>
suppose if I have a total 20 ns simulation with 4 breaks (i.e 5<br>
ns in each run), then there will be 4 .tpr files. So at the end<br>
of 20 ns if I wish to calculate RMSD, then which .tpr file<br>
should I suppy to g_rms, the first one or the last one? We I run<br>
g_rms with the two .tpr files, I get different results. So which<br>
one should be used? Any suggestion is welcome.<br>
<br>
<br>
Use the one that contains the structure you wish to serve as your<br>
reference.<br>
<br>
-Justin<br>
<br>
<br>
Thanks,<br>
<br>
Anirban<br>
<br>
<br>
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========================================<br>
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========================================<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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