[gmx-users] g_traj with xtc_grps ... all coordinates zero

[Mark Abraham]

When starting a new topic, please start a new email with a new subject 
line. Not only does this maximize the chance that people who know the 
answer to your problem will read about your problem, but you use 
everybody's time more efficiently.

ravi kant wrote:

> I am trying to study the properties of Argon by NVT simulation. The 
> configuration file of Ar which I generated fills the half of simulation 
> box (cuboid)  with Ar atoms and rests nothing.
> After running the simulation I found that some regions of cubiod 
> were highly packed with Ar compared to others. Then I tried g_energy to 
> find out diffusivity and other  parameters. But they were all giving 
> average values. Can you please tell me the way of finding the 
> diffusivity values within a small space eg. within a sphere, or box of 
> some dimension, inside the simulation box.

If there's nothing in the manpages for these tools suitable for what you 
want to do, then you're probably on your own.

Mark