[gmx-users] correlation function

[Justin A. Lemkul]

Jamie Seyed wrote:
> 
> 
> On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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??
>  

I think, if you average the ACF, you will get zero.

> --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?

Filtered trajectories are for visualization purposes only.  When doing analysis, 
always use the original trajectory.

-Justin

> Many Thanks/Jamie
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> 
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> 
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

========================================