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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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