[gmx-users] LINCS warnings
Mark.Abraham at anu.edu.au
Mon Jun 11 10:11:35 CEST 2012
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.
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