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

[ravi kant]

Hi all,

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.


Ravi
IIT Kanpur
India
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