[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 6 16:53:26 CEST 2012

On 7/6/12 10:40 AM, khandelia wrote:
> Justin, Vitaly
> The topology is fine, I double-checked
> The simulation runs perfectly fine without the restraints.
> It is not a PBC effect, since the box size along z is > 50 nm after a ns or
> so.
> Does one need yet another restraint to hold the bilayer together?

I have never had a need for any restraints to keep a bilayer intact.

> There has been some discussion about problems with dihedral restrains in the
> list earlier, but nothing like this.

The problem you're observing seems to indicate that your manipulation of the 
lipid chain causes physical instability.  How extensive are the restraints?  How 
many atoms do they involve?  You provided an "etc" in your previous message, so 
I'm trying to clarify what's going on.  Is it even physically possible to orient 
the lipid chain in such a way?  You've got basically all the consecutive 
dihedrals in a very specific orientation - is that compatible with your system? 
  Can you run a simulation of a single lipid in vacuo using these restraints?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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