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>> 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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