[gmx-users] Why my system collapsed?

Peggy Yao peggy.yao at gmail.com
Wed Apr 16 05:03:08 CEST 2008

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!

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