[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?
> http://gromacs.5086.n6.nabble.com/file/n4999393/POPC..jpg

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


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