[gmx-users] correlation function
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 23 02:02:45 CEST 2009
Jamie Seyed wrote:
> Hi Justin,
> Thanks again. I made and used coord.xvg with command
> g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that
> I think I need to average over it. Would you please let me know how I
> can get a nice average curve? Also I can see that all of them starting
> at 1, but I do not think the average is going to 0 finally (my system is
> 216 spce water, 20ps). Is this because the simulation time is not long
> enough?? Many Thanks in Advance/Jamie
>
Not sure, I've never tried such an analysis. 20 ps is pretty short, though.
Collecting a few ns of data on such a small system should be trivial.
Otherwise, give some indication of what's actually in the coord.xvg file;
someone may have an idea as to what's going on. I'm not clear what you're
exactly after, an average of the ACF?
-Justin
> On Sat, Aug 22, 2009 at 6:49 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> Hi Justin,
> Thanks for the answer. I want to calculate auto-correlation
> function of R(x,y,z). I mean <R(0).R(t)> , .../Many Thanks in
> Advance/Jamie
>
>
> Coordinates? Use g_traj.
>
> -Justin
>
> On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> Hi Mark,
>
> Thanks for the answers. I want to use g_analyze but it
> needs a
> file graph.xvg as an input file. How can I get that for
> calculation of auto-correlation function? Many Thanks in
> Advance/Jamie
>
>
> The graph.xvg file contains the data for which you want to obtain
> the autocorrelation function. Many of the Gromacs analysis tools
> produce .xvg files of whatever quantity they are measuring. I
> suppose it would then be important to figure out what type of
> data
> you are trying to obtain the autocorrelation function for;
> that will
> determine which tool to use :)
>
> -Justin
>
> On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>> wrote:
>
> Jamie Seyed wrote:
>
> Hi Mark,
> Thanks for the information. Actually in 7.4 I
> found only
> g_rotacf and
> g_angle also g_sgangle that calculate rotation and
> angle
> correlation
> function and in appendix D I could not find related
> topic... I
> appreciate if
> someone gives me more detail to do the job.
> I want to calculate <R(0).R(t)> that R is
> coordinates vector
> R(x,y,z) for
> pure spce water.
>
>
> If that's an auto-correlation function, then g_analyze
> does
> the job.
> Searching for "correlation" in the manual was a good
> way to
> start.
> That would also have found a whole section devoted to
> the topic,
> which is good reading.
>
>
> Also I have a question related to having a
> coordinate file. I
> did a command
> as
> trajconv -f md.trr -n f.ndx -o md.xtc
> I am supposing in this case md.xtc contains only x,y,z
> coordinates. Is that
> true?? Many Thanks in Advance/Jamie
>
>
> Yes, since the compression algorithm used for .xtc
> only works on
> positions. However it is a lossy compression, and if
> you want
> full-precision positions-only, look at the options in
> trjconv -h.
>
>
> Mark
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://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 <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
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