[gmx-users] correlation function
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Aug 23 02:19:46 CEST 2009
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>> 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>>> 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>>>> 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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