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
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