[gmx-users] correlation function
jamie.seyed at gmail.com
Sun Aug 23 16:30:51 CEST 2009
Thanks for the answers. Please check below...
On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> Jamie Seyed wrote:
>> Hi Justin and Mark,
>> Thanks. Actually I made a mistake and it seems going to the zero
>> (even negative!)
>> --But I wanted to know how I can write my command to get only
>> one graph (average of all instead of all of them). I read the
>> manual chapter-8 and by average I mean I should get one curve
>> starting at 1 and coming down to zero...I also tried
>> That's not an average; that's the shape of the ACF curve.
>> Yes I need to get that shape using g_analyze..!.
> Right, I just don't understand why you think you need to obtain some sort
> of average. What do you mean by "all of them"? How many graphs are there?
Actually when I open autocorr.xvg I can see from data/feature extraction/
the last set is S1295 (N=101, autocorr.xvg) which means they are 1296
graphs each with poor statistics start at 1 and coming down. To have a ACF
for a system I expect to get one graph with good statistic... I hope I make
it clear now.
> No, only ACF based on coordinates. I read from the list that people said I
>> can use g_rotacf -d for calculation of correlation functions...and actually
>> I did it for a simple system. But for new system using another index file it
>> is complaining.
> Then I don't think g_rotacf is the tool you want. There is no magic way to
> simply calculate some sort of general correlation function. You calculate
> an ACF from the specific data you have. So if you're interested in some
> sort of position-dependent data, then rotational properties may or may not
> be relevant.
> You can certainly use g_rotacf if you think it will be meaningful; see
> below regarding your .tpr file.
> tpbconv -s f.tpr -f f.trr -n f.ndx -o tpxout.tpr
> Don't use -f. If you do, tpbconv will think you are trying to create a new
> .tpr file that starts off from the time frame present in the .trr file.
Yes I removed -f and I got tpxout.tpr and used it for g_rotacf
g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d
but the result I got is like y=2x that starts at (0,0) which y=C(t) and
x(Time,ps). Which is very strange... I don't understand what are these
results using this command. (I should mention that f.xtc contains the
coordinates of selected atoms). Many thanks for your attention and your
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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