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

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 4 18:23:18 CEST 2008

Quoting maria goranovic <mariagoranovic at gmail.com>:

> Dear All
> I am running a 128-lipid bilayer simulation with standard parameters. The
> simulation abruptly crashed after 2 ns, and a look into the pdb files
> suggested that bonds were being broken and eventually the lipids explode. I
> tried increasing the cutoffs from 1.0 to 1.4, and this time also, the
> simulation exploded, but at a different time point.
> The energy remains nice and stable till the explosion.
> How does one fix this ? What is planting these bombs ?

You'll have to describe how you minimized and equilibrated your bilayer before
we'll have any idea what's going on.  Also have a thorough look through the
archives; many users have posted about bilayers exploding (including yours


> Thank you for suggestions.
> --
> Maria G.
> Technical University of Denmark
> Copenhagen


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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