[gmx-users] LINCS warnings

[Mark Abraham]

On 11/06/2012 5:49 PM, rama david wrote:
> Hi MARK,
>  Thank you to your  Quick reply,
> Please accept my apology for incomplete information...
>
>  I did simulationm of single, Double and four peptide..
>
> I also tried following
> I make antiparrallel arrangment of four peptide with distance of 0.4 
> nm in y direction,
> Then I translate these layer  in z direction, Such that separation in 
> each layer is 0.4 ,
>
> I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ),
> All things was right.

Well you'll have to follow the kind of advice in the diagnostic section 
of the link I gave last time. Since your topology is apparently sound, 
the initial conditions are likely suspect. Be sure you have visualized 
them, and that the box around them is definitely big enough.

Mark