<div>Hi Justin,</div>
<div>Thanks again. I made and used coord.xvg with command </div>
<div>g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starting at 1, but I do not think the average is going to 0 finally (my system is 216 spce water, 20ps). Is this because the simulation time is not long enough?? Many Thanks in Advance/Jamie<br>
<br></div>
<div class="gmail_quote">On Sat, Aug 22, 2009 at 6:49 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>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Justin,<br>Thanks for the answer. I want to calculate auto-correlation function of R(x,y,z). I mean <R(0).R(t)> , .../Many Thanks in Advance/Jamie<br>
<br></blockquote><br></div>Coordinates? Use g_traj.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<div></div>
<div class="h5">On Sat, Aug 22, 2009 at 6:40 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> Hi Mark,<br><br> Thanks for the answers. I want to use g_analyze but it needs a<br> file graph.xvg as an input file. How can I get that for<br> calculation of auto-correlation function? Many Thanks in<br>
Advance/Jamie<br><br><br> The graph.xvg file contains the data for which you want to obtain<br> the autocorrelation function. Many of the Gromacs analysis tools<br> produce .xvg files of whatever quantity they are measuring. I<br>
suppose it would then be important to figure out what type of data<br> you are trying to obtain the autocorrelation function for; that will<br> determine which tool to use :)<br><br> -Justin<br><br> On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> wrote:<br><br> Jamie Seyed wrote:<br><br> Hi Mark,<br> Thanks for the information. Actually in 7.4 I found only<br>
g_rotacf and<br> g_angle also g_sgangle that calculate rotation and angle<br> correlation<br> function and in appendix D I could not find related<br> topic... I<br> appreciate if<br>
someone gives me more detail to do the job.<br> I want to calculate <R(0).R(t)> that R is coordinates vector<br> R(x,y,z) for<br> pure spce water.<br><br><br> If that's an auto-correlation function, then g_analyze does<br>
the job.<br> Searching for "correlation" in the manual was a good way to<br> start.<br> That would also have found a whole section devoted to the topic,<br> which is good reading.<br>
<br><br> Also I have a question related to having a coordinate file. I<br> did a command<br> as<br> trajconv -f md.trr -n f.ndx -o md.xtc<br> I am supposing in this case md.xtc contains only x,y,z<br>
coordinates. Is that<br> true?? Many Thanks in Advance/Jamie<br><br><br> Yes, since the compression algorithm used for .xtc only works on<br> positions. However it is a lossy compression, and if you want<br>
full-precision positions-only, look at the options in trjconv -h.<br><br><br> Mark<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></div></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>>
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<div class="im"> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br>
</div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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<div class="h5">========================================<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>
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