[gmx-users] correlation function
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 23 02:44:12 CEST 2009
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.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>>
> <mailto: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>>>
> <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
> <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/> <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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--
========================================
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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