[gmx-users] Supradiffusivity in a bilayer
quantrum75 at yahoo.com
Tue Oct 11 14:27:40 CEST 2005
Your advice has been quite invaluable. Even from the
--- Erik Lindahl <lindahl at sbc.su.se> wrote:
> On Oct 10, 2005, at 5:10 PM, Rama Gullapalli wrote:
> > Dear GMX ers
> > I had a simple question regarding the calculation
> > lipid diffusion.
> > 1) How do i remove the supradiffusivity of the
> > 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
> > 2) How do i couple the COM removal of the
> > bilayer leaflets while running the simulation? Is
> > through make_ndx, assign names and couple them
> > seperately? Also, is it necessary to do the same
> > 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 :-)
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