[gmx-users] Trajectory Analysis!

[chiloo Laohpongspaisan]

 Dear all,
 
there is an error as follows:
---------------------------------------------------------
Group     0 (    Nitrogen) has     2 elements
There is one group in the index
Will gather information on 1 bonds
Last frame       2000 time 7000.000
Total number of samples               : 2001
Mean                                  : 1.10008
Standard deviation of the distribution: 0.0655399
Standard deviation of the mean        : 0.00146515
Back Off! I just backed up dNN.xvg to ./#dNN.xvg.1#
Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
--------------------------------------
i 'd like to investigate distance between Nitrogen atom.
This is the command that i used:
 g_bond -f md7.xtc -n index.ndx -s md7.tpr -o dNN.xvg -l dNN.log -d dNN.xvg

And This is my index file:
 
[ Nitrogen ]
129 597

PLease suggest me, what' s wrong?
 
Best regards,
Chiloo
leafyoung81-group at yahoo.com wrote:
--- chiloo Laohpongspaisan wrote:

> Dear All,
> 
> If i'd like to investigate the distance between 2
> atoms of the system (protein/bilayer/water), is the
> command "g_bond"? And are there any options that
> must be added to focus only two atoms.
Yes. put two atoms into one group of the index file
and specify the index file (with -n) for g_bond

> And If i'd like to investigate the movement of one
> water molecule, how is the command?
similarly, put the water molecule into one group of
the index file and specify the index file (with -n)
for g_trjconv to get the trajectory.
> 
> Best regards,
> chiloo
> 
> 
> 
> 
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