[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode
Mark.Abraham at anu.edu.au
Mon Apr 7 10:02:20 CEST 2008
maria goranovic wrote:
> Sorry for the incomplete details. Here they are now:
> I started with a well-equilibrated POPC bilayer, and changed one POPC
> lipid to a lipid of my interest. I wrote the topology file for the new
> lipid accordingly.
This topology change is probably the source of the problem, and would
have been a good thing not to describe as "a 128-lipid bilayer
simulation with standard parameters".
> After that, I did some simple steepest descent minimization, and
> followed it up by dynamics. Here is the .mdp file for the runs. There is
> a preceding 25,000-step simulation where the initial velocities are
> assigned. The mdp file below is what is being used for equilibrium dynamics.
That's all fine. You should have a close look at the structures leading
up to the simulation crashes, and pay attention to all of the warning
messages from grompp and error messages from mdrun.
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