[gmx-users] Unsupported box diagonal

[Sweta Iyer]

Hi,
I am trying to do a simple membrane simulation of a h4 residue helix in
DMPC. However, I encounter a strange issue this time when i try to run the
final production run. the error that i get is as follows:

Check for bad contacts and/or reduce the timestep.

WARNING: Unsupported box diagonal 6.178595 6.197406 -0.367044, will not
use periodic boundary conditions

WARNING: Unsupported box diagonal 6.178595 6.197406 -0.367044, will not
use periodic boundary conditions



So i went back and checked the gro file and removed all possible waters or
lipid atoms that may have been close to the protein and still it remains
the same. My box diagonal as shown in the gro after em is 6.30580  
6.32500   8.42100.
However,after positional restraint dynamics my coordinates are 6.17859  
6.19740   7.87826. I wonder why this change occurs.

Thank you for your time.




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