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<div class="gmail_quote">On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">with a lot of x-y sets seperated by & character. I think I did not get the key point here. So my question is what is the right way to get <R(0)R(t)> using this tool?? Many Thanks/Jamie<br>
</blockquote><br></div>Well, as far as g_analyze is concerned, it's done its job. If you feed g_analyze a whole bunch of data sets, it will give you a whole bunch of ACF's. So you essentially got an ACF for each molecule's x, y, and z coordinates. I guess I just don't understand what you're really after, because as I said, g_analyze did its job. </blockquote>
<div> </div>
<div>Thanks a lot Justin,</div>
<div>Actually I tried to use xmgrace to make a <> of all bunch of ACF and I find under data/feature extraction/Feature Y average to do the job. I did not find out how it works yet, but do you think is this correct??</div>
<div> </div>
<div>--another question related to g_rotacf. Before I used it like this:</div>
<div>first I made a ndx file and then extract xtc and tpr file for ndx and then used this command:</div>
<div> </div>
<div>1) g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d </div>
<div>and I saw strange result (as I mentioned before like y=2x)</div>
<div>Then I tried to use original files (xtc and tpr) insted of filtered files:</div>
<div> </div>
<div>2) g_rotacf -f traj.xtc -s f.tpr -n f.ndx -o rotacf.xvg -d </div>
<div>and I got completely different but very expected result. So now I believe that the right way is the second one... Do you have any idea or comment on this? or what is the result of first method?</div>
<div>Many Thanks/Jamie<br><br>-Justin<br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080
<div class="im"><br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>
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