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