[gmx-users] correlation function
jamie.seyed at gmail.com
Mon Aug 24 21:59:18 CEST 2009
On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Jamie Seyed wrote:
> with a lot of x-y sets seperated by & character. I think I did not get the
>> key point here. So my question is what is the right way to get <R(0)R(t)>
>> using this tool?? Many Thanks/Jamie
> Well, as far as g_analyze is concerned, it's done its job. If you feed
> g_analyze a whole bunch of data sets, it will give you a whole bunch of
> ACF's. So you essentially got an ACF for each molecule's x, y, and z
> coordinates. I guess I just don't understand what you're really after,
> because as I said, g_analyze did its job.
Thanks a lot Justin,
Actually I tried to use xmgrace to make a <> of all bunch of ACF and I find
under data/feature extraction/Feature Y average to do the job. I did not
find out how it works yet, but do you think is this correct??
--another question related to g_rotacf. Before I used it like this:
first I made a ndx file and then extract xtc and tpr file for ndx and then
used this command:
1) g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d
and I saw strange result (as I mentioned before like y=2x)
Then I tried to use original files (xtc and tpr) insted of filtered files:
2) g_rotacf -f traj.xtc -s f.tpr -n f.ndx -o rotacf.xvg -d
and I got completely different but very expected result. So now I believe
that the right way is the second one... Do you have any idea or comment on
this? or what is the result of first method?
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
> jalemkul[at]vt.edu | (540) 231-9080
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