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
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