[gmx-users] Question about applying a restriction on the movement of a molecule in z direction....

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jun 13 02:39:44 CEST 2009

Alberto Sergio Garay wrote:
> Hi all
> I need to avoid that a solute molecule cross to the other side of my 
> lipid bilayer.and I have thought in several alternatives, which I'm not 
> sure whether they are posible in gromacs so I decided to ask for 
> suggestions.

In a periodic system with one symmetric bilayer and one block of 
solvent, there seems to be little value in such a restriction.

> Could anyone give any possible alternative to restrict the movement of 
> my molecule in the z direction only when it reaches a certain z distance 
> from, for example the center of the bilayer ?

Pick a few key atoms in the bilayer, decide how far you want to let it 
roam from the bilayer, do your Pythagoras and work out the maximum 
displacement from a key atom that is consistent with your maximum 
bilayer displacement, invoke a fudge factor, and use distance restraints 
on those key atoms.


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