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 <jalem...@vt.edu
<mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@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/> | (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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