[gmx-users] correlation function
Jamie Seyed
jamie.seyed at gmail.com
Sun Aug 23 01:01:56 CEST 2009
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. Would you please let me know how I can get
a nice 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
On Sat, Aug 22, 2009 at 6:49 PM, Justin A. Lemkul <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>> 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>>> 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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