[gmx-users] correlation function

Mark Abraham Mark.Abraham at anu.edu.au
Sun Aug 23 02:46:16 CEST 2009

Jamie Seyed wrote:
> 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).

We can't know either, because you haven't told us what you're looking 
for. Read "g_analyze -h", of course.

> --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.

Read "tpbconv -h". There are multiple uses for tpbconv, and it looks 
like the order of the error-checking is inconvenient for your situation. 
So use -extend arbitrarily. You're not using this file for simulation, 
so that doesn't matter.

> 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

Some analysis tools will accept any structure file, and some require a 
run input file. Look at the acceptable file types for -s in "g_rotacf -h".


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