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

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


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