[gmx-users] Supradiffusivity in a bilayer
lindahl at sbc.su.se
Mon Oct 10 19:23:02 CEST 2005
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users