[gmx-users] removing a water molecule

[Mark Abraham]

Ragothaman Yennamalli wrote:
> Thanks.
> I do get LINCS warning all the time. I had removed two
> water molecule, that seemed too close to where the
> LINCS warning came for. And started the simulation
> again from the scratch and it stopped as mentioned in
> my previous message.

Yup. Go and fix your equilibration regime (copy something reasonable 
from a published paper or a tutorial). A normal simulation should have 
no LINCS errors.

Mark