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<div class="gmail_quote">On Sun, Aug 23, 2009 at 7:32 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><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> Actually when I open autocorr.xvg I can see from data/feature<br> extraction/ the last set is S1295 (N=101, autocorr.xvg) which means<br>
they are 1296 graphs each with poor statistics start at 1 and coming<br> down. To have a ACF for a system I expect to get one graph with good<br> statistic... I hope I make it clear now. <br></blockquote><br></div>
What did you extract with g_traj? All the coordinates of all the molecules? The command line you gave would be helpful here. It would seem that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is trying to calculate some sort of ACF between all coordinates: x-x, y-y, z-z, x-y, x-z, y-z. That way, you'd be getting these ACF's for each individual molecule. Again, just a guess. </blockquote>
<div> </div>
<div>Hi Justin,</div>
<div>I think that I extract only the coordinates for my desired atoms using this command:</div>
<div>g_traj -f f.xtc -s f.tpr -n f.ndx -ox coord.xvg </div>
<div>and then</div>
<div>g_analyze -f coord.xvg -ac autocorr.xvg</div>
<div> </div>
<div>Is that the way to get ACF or I am doing something wrong here?? Many Thanks in Advance/Jamie</div>
<div> </div>
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<div class="h5"><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>
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>
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