[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 18:44:06 CEST 2008


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> 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.

And as an aside, broken bonds are only a visualization effect; mdrun doesn't
write broken molecules.  Also, providing your .mdp file would be of use.

-Justin

> >
> > 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
> truly).
>
> -Justin
>
> >
> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================



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