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<div>Yah but you'll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).</div>
<div> </div>
<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Mittwoch, 21. Mai 2014 um 06:54 Uhr<br/>
<b>Von:</b> "tarak karmakar" <tarak20489@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] entropy vs time plot</div>
<div name="quoted-content">Hi Tsjerk,<br/>
Thanks for the quick reply.<br/>
I did the following<br/>
<br/>
g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v<br/>
eigenvec.trr -av average.pdb -b 0 -e 10000<br/>
g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 10000<br/>
<br/>
What I want to plot is similar to this.<br/>
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/" target="_blank">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304994/figure/fig4/</a><br/>
<br/>
Is there any flag for this?<br/>
I've checked g_covar -h and g_anaeig -h but didn't get the proper way.<br/>
<br/>
Thanks,<br/>
Tarak<br/>
<br/>
<br/>
<br/>
On Tue, May 20, 2014 at 11:04 PM, Tsjerk Wassenaar <tsjerkw@gmail.com>wrote:<br/>
<br/>
> Hi Tarak,<br/>
><br/>
> You will have to use -b/-e to set the start and end times.<br/>
><br/>
> Cheers,<br/>
><br/>
> Tsjerk<br/>
><br/>
><br/>
> On Tue, May 20, 2014 at 12:18 PM, tarak karmakar <tarak20489@gmail.com<br/>
> >wrote:<br/>
><br/>
> > Dear All,<br/>
> > Could anyone tell me how to plot configurational entropy as a function of<br/>
> > simulation time?<br/>
> > Do I need to manually specify the -dt(say after each 1 ns) during the<br/>
> > g_covar and then do g_anaeig in each of the step?<br/>
> ><br/>
> > thanks,<br/>
> > Tarak<br/>
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><br/>
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> Tsjerk A. Wassenaar, Ph.D.<br/>
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