[gmx-users] Trajectory Analysis!

[leafyoung81-group at yahoo.com]

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