[gmx-users] correlation function
Jamie Seyed
jamie.seyed at gmail.com
Sun Aug 23 02:37:55 CEST 2009
Hi Justin and Mark,
Thanks. Actually I made a mistake and it seems going to the zero (even
negative!)
--But I wanted to know how I can write my command to get only one graph
(average of all instead of all of them). I read the manual chapter-8 and by
average I mean I should get one curve starting at 1 and coming down to
zero...I also tried
g_analyze -f coord.xvg -ac autocorr.xvg -av average.xvg
but I do not know what is this average file (it is not clearly what I am
looking for).
--Also for the same purpose I tried g_rotacf -d ,
first I extract the coordinates of selected atoms into f.xtc and then tried
this command:
g_rotacf -f f.xtc -s f.tpr -n f.ndx -o retacf.xvg -d
I got an error message that : " Molecule in topology has atom numbers below
and above natoms. you are
probably trying to use a trajectory which does not match the first 330 atoms
of the run input file. You can make a matching run input file with *tpbconv*
."
But when I used tpbconb to generate new tpr file using my index file,
without giving an error it says "0 steps (0 ps) remaining from first run.
You have simulated lon enough. not writing tpr file" and nothing has been
generated.
I read this problem from mailing list and people said that I can use pdb/gro
file instead. So I modified last gro file and kept the same atoms as my
index file (ref.gro) and used it instead of tpr file:
g_rotacf -f f.xtc -s ref.gro -n f.ndx -o retacf.xvg -d
But Can not open ref.gro.tpr
So I do not know how to get rid of this error...Thanks in Advance/Jamie
On Sat, Aug 22, 2009 at 8:19 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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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