[gmx-users] Supradiffusivity in a bilayer

[Rama Gullapalli]

Dear Erik
Your advice has been quite invaluable. Even from the
archives...
Thanks
Regards
Rama

--- Erik Lindahl <lindahl at sbc.su.se> wrote:

> Hi,
> 
> On Oct 10, 2005, at 5:10 PM, Rama Gullapalli wrote:
> 
> > Dear GMX ers
> > I had a simple question regarding the calculation
> of
> > lipid diffusion.
> >
> > 1) How do i remove the supradiffusivity of the
> bilayer
> > when calculating the diffusion constant?
> 
> If you haven't started the simulation yet, define
> three separate  
> groups for center-of-mass motion removal: water and
> a separate group  
> for each lipid layer.
> 
> If you already started it, you can use a trick that
> might require  
> some coding. Go through the trajectory, remove
> periodicity and  
> calculate the center-off-mass for each frame.
> Calculate how much the  
> COM moves, and then remove this motion from each
> frame.
> 
> >
> > 2) How do i couple the COM removal of the
> individual
> > bilayer leaflets while running the simulation? Is
> it
> > through make_ndx, assign names and couple them
> > seperately? Also, is it necessary to do the same
> in
> > order to obtain correct diffusion coefficients?
> 
> You've essentially got it :-)
> 
> The COM motion needs to be taken into account one
> way or the other,  
> since the periodic system means there isn't any
> natural friction for  
> collective XY motion. Doing it before is easier, but
> we managed to  
> publish the first reasonably accurate diffusion
> constants by coming  
> up with the second method - 100ns of trajectories
> was a lot at the  
> time, and we weren't exactly thrilled with the idea
> of rerunning it  
> all :-)
> 
> Cheers,
> 
> Erik
> 
> 
> 
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