[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Mark.Abraham at anu.edu.au
Tue Jul 24 07:09:08 CEST 2012
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.
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