[gmx-users] removing a water molecule

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 28 08:59:53 CEST 2007

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.


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