[gmx-users] Unsupported box diagonal

[Mark Abraham]

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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