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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