[gmx-users] Trajectory Analysis!

[leafyoung81-group at yahoo.com]

--- chiloo Laohpongspaisan <chiloo77 at yahoo.com> wrote:

>  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?
Nothing wrong but bond distance has been very stable.
>  
> 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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