[gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode

[Mark Abraham]

maria goranovic wrote:
> Hi,
> 
> 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.

Mark