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<div class="gmail_quote">On Sun, Aug 23, 2009 at 10:30 AM, Jamie Seyed <span dir="ltr"><<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@gmail.com</a>></span> wrote:<br>
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<div>Hi Justin,</div>
<div>Thanks for the answers. Please check below...
<div class="im"><br><br>On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><br></div></div>
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<div><br><br>On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> Jamie Seyed wrote:<br><br></div>
<div> Hi Justin and Mark,<br> Thanks. Actually I made a mistake and it seems going to the zero<br> (even negative!)<br> --But I wanted to know how I can write my command to get only<br> one graph (average of all instead of all of them). I read the<br>
manual chapter-8 and by average I mean I should get one curve<br> starting at 1 and coming down to zero...I also tried<br> <br><br> That's not an average; that's the shape of the ACF curve.<br>
<br> Yes I need to get that shape using g_analyze..!.<br></div></blockquote><br>Right, I just don't understand why you think you need to obtain some sort of average. What do you mean by "all of them"? How many graphs are there?</blockquote>
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<div>Actually when I open autocorr.xvg I can see from data/feature extraction/ the last set is S1295 (N=101, autocorr.xvg) which means they are 1296 graphs each with poor statistics start at 1 and coming down. To have a ACF for a system I expect to get one graph with good statistic... I hope I make it clear now. </div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">No, only ACF based on coordinates. I read from the list that people said I can use g_rotacf -d for calculation of correlation functions...and actually I did it for a simple system. But for new system using another index file it is complaining.<br>
<br></blockquote><br></div>Then I don't think g_rotacf is the tool you want. There is no magic way to simply calculate some sort of general correlation function. You calculate an ACF from the specific data you have. So if you're interested in some sort of position-dependent data, then rotational properties may or may not be relevant.<br>
<br>You can certainly use g_rotacf if you think it will be meaningful; see below regarding your .tpr file.<br><br><snip>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">tpbconv -s f.tpr -f f.trr -n f.ndx -o tpxout.tpr<br> <br></blockquote><br></div>Don't use -f. If you do, tpbconv will think you are trying to create a new .tpr file that starts off from the time frame present in the .trr file.</blockquote>
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<div>Yes I removed -f and I got tpxout.tpr and used it for g_rotacf </div>
<div>g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d</div>
<div>but the result I got is like y=2x that starts at (0,0) which y=C(t) and x(Time,ps). Which is very strange... I don't understand what are these results using this command. (I should mention that f.xtc contains the coordinates of selected atoms). Many thanks for your attention and your help/Jamie</div>
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<div>Please ignore this part since I used wrong files.../Thanks, Jamie</div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span></span><br><font color="#888888"><br>-Justin</font>
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<div><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>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<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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