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

[J Peterson]

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?

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 

Thanks

Peterson


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