[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin A. Lemkul]

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

-- 
========================================

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

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