[gmx-users] Equilibrated system explodes after ~200ns?

Trayder trayder.thomas at monash.edu
Mon May 6 09:36:24 CEST 2013

Hi all,
My simulation is composed of 2 protein chains wrapped around a lipid disk
composed of a dozen different lipid types, water and ions in a 15nm cube.
The protein encircles the mixed composition lipid disk.
I've got 4 duplicate simulations with velocities generated from a different
random seed.
The starting structure for these simulations was taken from the end of a
previous 200ns simulation (same settings but bigger box) which ended
I am using gromacs 4.6, with the gromos54a7 force field. No gpus.

The first simulation exploded (a few atoms fly off into the distance leaving
the rest intact) shortly before 150ns, two more have crashed shortly before
200ns. 1 is still running. Restarting a simulation has it crash at a
different point.

Over 3 steps of escalating LINCS warnings I get a warning followed by a
fatal error

The atoms initially involved in the LINCS warnings correspond to atoms
around a double bond in a single lipid tail. Specifically in linoleic and
linolenic (2 or 3 double bonds in sequence). The parameters used were
adapted from the packaged POPC parameters using the same bond types from

Energy graphs seem to indicate that the system is equilibrated.
Does anyone have any ideas what's going on here?
Thanks in advance,

P.S. mdp file

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