[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 13 06:27:18 CEST 2012
On 7/13/12 12:24 AM, J Peterson wrote:
> Hi Justin,
> I followed your comments and now at the stage of adding solvents.
> I wonder to see the protein after shrinking step to have no SOL molecules as
> there were SOL molecules in the source popc128b.pdb. Had we removed all the
> original SOL molecules anywhere during the course of tutorial?
InflateGRO removes all solvent molecules.
> I also see one of the POPC molecules standing out (upside down) of the
> bilayer area. How would that be adjusted?
You need a bigger box. The lipids are moving into a neighboring periodic cell,
which in itself is not a problem, but I suspect you'll have inadequate hydration
and thus you'll be calculating headgroup-headgroup interactions across periodic
boundaries, which you probably want to avoid.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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