[gmx-users] GPU running problem with GMX-4.6 beta2

[Albert]

On 12/17/2012 08:06 PM, Justin Lemkul wrote:
> It seems to me that the system is simply crashing like any other that 
> becomes unstable.  Does the simulation run at all on plain CPU?
>
> -Justin 


Thank you very much Justin, it's really helpful. I've checked that the 
structure after minization and found that there is some problem with my 
ligand. I regenerated the ligand toplogy with acpype, and resubmit for 
mimization and NVT. Now it goes well. So probably the problems comes 
from the incorrect ligand topolgy which make the system very unstable.

best
Albert