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.
g_analyze -f coord.xvg -ac autocorr.xvg -av average.xvg
but I do not know what is this average file (it is not clearly what I am
looking for).
The average.xvg file contains the average of the values in coord.xvg, a simple
statistical analysis.
--Also for the same purpose I tried g_rotacf -d ,
first I extract the coordinates of selected atoms into f.xtc and then
tried this command:
g_rotacf -f f.xtc -s f.tpr -n f.ndx -o retacf.xvg -d
I got an error message that : " Molecule in topology has atom numbers
below and above natoms. you are
probably trying to use a trajectory which does not match the first 330 atoms
of the run input file. You can make a matching run input file with
*tpbconv*."
Before you were describing trying to calculate some sort of ACF based on
coordinates, now you are trying to calculate a rotational ACF. What type of
data are you actually trying to collect? All of the above?
But when I used tpbconb to generate new tpr file using my index file,
without giving an error it says "0 steps (0 ps) remaining from first
run. You have simulated lon enough. not writing tpr file" and nothing
has been generated.
What command are you giving tpbconv? By giving only your .tpr and .ndx files,
you should be able to write out a new .tpr file of a subset of atoms.
I read this problem from mailing list and people said that I can use
pdb/gro file instead. So I modified last gro file and kept the same
atoms as my index file (ref.gro) and used it instead of tpr file:
g_rotacf -f f.xtc -s ref.gro -n f.ndx -o retacf.xvg -d
But Can not open ref.gro.tpr
So I do not know how to get rid of this error...Thanks in Advance/Jamie
g_rotacf requires a .tpr file; this should be clear from g_rotacf -h (and from
the error message itself). Not every post in the list archive is accurate :)
-Justin
On Sat, Aug 22, 2009 at 8:19 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
Justin A. Lemkul wrote:
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.
Huh? The average has nothing to do with calculating the
autocorrelation function. There's a nice long section in the manual
about correlation functions. Read it.
Would you please let me know
how I can get a nice average curve?
Define "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
I don't understand your statement.
Mark
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>
<mailto: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>>
<mailto: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>>>
<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
<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/> <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/> <http://vt.edu/> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
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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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