[gmx-users] correlation function

Jamie Seyed 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?
Many Thanks/Jamie



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA

> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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