[gmx-users] Freeze all beyond a sphere

[Tivadar Orban]

Dear gromacs users,
I want to see the differences, reliability, of a system when I simulate it
with the following approch:
1. Simulate (1ns) without any frozen group (this is all right)
2. Freeze all atoms from the system that are beyond a sphere with the center
fixed on a specific atom (in my case the center is FE from the heme), and a
given ray.
3. I want to take different values of the ray and perform on each of them a
simulation.
4. after that compare the results obtained with diff ray spheres.
For this I wrote a short program that takes out all atom numbers (from the
.gro file that I use before running grompp MD and after mdrun MD) where the
distance between the atom A(i) and Fe is bigger than the chosen ray.
The atom numbers are added in the index.ndx file after a group named
RIsBigger.
The mdp file that I have has the

 
freezegrps = RIsBigger
Freezedim = Y Y Y

For mdrun I specify the new index.ndx file.

After running I get the following error:
Water molecule 4756 cannot be settled.

This is the first one, the second one:
For a specific ray the simulation went smoothly, but after simulation I saw
that the .gro file after mdrun instead of having numerical values has NaN,
not for all rows but a lot of them.

Could anybody give me a hint?

Regards,

Tivadar, Orban