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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What have you tried with g_analyze so far? What was your result? Is it what you expect? If not, why isn’t it what you expect?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Trying something out is far faster and you learn more than waiting for a response from others that don’t know exactly what you are doing.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><br>
At a first look, the command you want to run is <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">g_analyze –f data.xvg –ac autocorr.xvg<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">as you have a data file with time (x) and variable (y) data and you want the autocorrelation function of the variable data. Have you tried that command?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>aiswarya pawar<br>
<b>Sent:</b> Tuesday, 27 September 2011 3:11 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] g_analyze doubt<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Mark,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">On 26/09/2011 5:10 PM, aiswarya pawar wrote:<o:p></o:p></p>
<p class="MsoNormal">HI Mark,<br>
<br>
i have a .xvg data for the distance of two atoms in each time frame.<br>
<br>
<br>
0.000000e+00 7.191033e-01<br>
1.000000e+00 7.304224e-01<br>
2.000000e+00 8.983867e-01<br>
3.000000e+00 8.779736e-01<br>
4.000000e+00 8.236583e-01<br>
5.000000e+00 8.298320e-01<br>
6.000000e+00 7.703011e-01<br>
7.000000e+00 8.569826e-01<br>
8.000000e+00 7.428180e-01<br>
9.000000e+00 7.487683e-01<br>
1.000000e+01 8.106729e-01<br>
1.100000e+01 8.702058e-01<br>
1.200000e+01 8.823072e-01<br>
1.300000e+01 8.902194e-01<br>
1.400000e+01 6.122664e-01<br>
1.500000e+01 5.804662e-01<br>
1.600000e+01 6.207849e-01<br>
1.700000e+01 4.852896e-01<br>
1.800000e+01 5.297776e-01<br>
1.900000e+01 5.432515e-01<br>
2.000000e+01 5.888653e-01<br>
2.100000e+01 4.620140e-01<br>
<br>
<br>
Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Have you read g_analyze -h and tried it out?<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
Mark<br>
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