[gmx-users] PBC fix for visualization

[Mohsen Ramezanpour]

Dear Gromacs users,

I have an HII phase made of one inverted cylinder (and waters inside) in a
triclinic box with 90, 90, 60 angles. After running the simulation, this
cylinder become bent like a curve. I.e. is not a perfect cylinder anymore.
As a result, some water molecules and lipids pass the box sides and enter
from the other side of box because of PBC.
Now, I want to make the cylinder again but I am not sure how to do so.

The best I could do was to use "-pbc mol  -ur compact" options in trjconv.
However, here are still some lipids and molecules which are not part of the
cylinder.

Any idea how could I fix the effect of these PBC in visualization?

Thanks
Mohsen

-- 
*Rewards work better than punishment ...*