[gmx-users] correlation function

[Jamie Seyed]

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

On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul <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>> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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