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

[Mark Abraham]

On 24/07/2012 2:57 PM, J Peterson wrote:
> Hi Justin,
>
> That works really fine and thanks.
>
> Now, how can I add additional SOL molecules only one side of the bilayer
> (either upper or lower)? Since my protein binds at the outer side
> (extracellular region) of the membrane I can only fill the upper
> (extracellular) region with SOL molecules instead of adding them also inside
> the membrane, to reduce the system size ?
>
> Can we do magic here with any commands to add SOL molecules only single side
> of the membrane?

Yes, but you'll need solvent on both sides else you're not modelling a 
solvated bilayer and will have to argue why your results are relevant. 
Further, if the z-direction is periodic then there is only one side to 
your bilayer anyway...

If you really want to remove the solvent, and your bilayer is oriented 
parallel to the xy-plane, then there's several techniques that can 
filter solvent molecules based on their z-coordinate. Simplest is 
removing them by hand in a text editor, but g_select can make an index 
group that trjconv can remove.

Mark