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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto: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/> <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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