[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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