[gmx-users] Why my system collapsed?

[Mark Abraham]

Peggy Yao wrote:
> Dear all,
>  
> I've run this simulation twice, but got exactly the same error. 
> Everything was fine up to position restrained simulation. However, the 
> MD simulation was not successful. The final error is:
>  
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
> -------------------------------------------------------
> Starting from step 1749465 (3498.93 ps), more and more bonds that 
> rotated more than 30 degrees appeared. Starting from step 1749466, the 
> warning "pressure scaling more than 1%, mu: 1.27191e+06 1.27191e+06 
> 1.27191e+06" started to appear, and the system collapsed at step 1749467.
>  
> Does anyone have idea what might be wrong? I was simulating a 
> calcium-binding protein with calcium atoms in water for 4ns. Thanks!

http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25

http://wiki.gromacs.org/index.php/blowing_up

Basically, there's something about your system setup (.mdp options, 
topology, starting structure) that leads to non-physical behaviour. Look 
closely at the early part of the simulation and see where things start 
going wrong. Pay attention to warnings from grompp - they're not decorative!

Mark