On 8/03/2011 3:58 PM, Sweta Iyer wrote:
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:
Looks like you haven't equilibrated well enough, e.g. you're simulating
at NPT and the volume changes are too severe.
Mark
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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