[gmx-users] pme/cutoff in membrane proteins
tieleman at ucalgary.ca
Fri Mar 8 20:25:55 CET 2002
Maybe some recent simulations we have done might be of interest for the
current discussions on PME etc.
We (me, Berk, Mark Sansom) have done simulations of a model six-helix
bundle that forms a water channel, comparing water-ordering with
reaction field, cutoff, PME, with the protein fixed. I think this should
be relevant for many membrane protein simulations. Cutoffs give very
strong water ordering, which seems consistent with tests Berk published
that show long-range correlations that get worse as your cutoff length
increases. PME and reaction field give similar order in most places, but
not in a few parts in the channel where there are long ranged
electrostatic effects, most probably due to the strong field generated
by the protein (6 parallel helices). I agree with some previous comments
that reaction fields are a bad idea in membrane proteins, simply because
they assume a homogeneous solution. This isn't all that true for
water-soluble proteins (maybe unless they're really small), it's
certainly not true for membrane proteins. They'd do funny things if you
would look at ion channels with ions seperated by a distance of the
order of your cutoff. Although there will be some papers coming out from
me that didn't use PME or PPPM, I now think that is less than a good
idea and is really mainly because it takes so long to finish a project.
To Erik's comment on lipids: we have some test simulations of 150 ns
that should show converged areas and structural properties, and the
effects of PME vs cutoff are pretty large, at least several percent in
areas for fully hydrated DPPC. Although we have one very big membrane
protein simulation running without PME at the moment because of the bad
scaling, everything else is using PME.
One other anecdote: in my tests of helix bundles, I tried a simulation
of a helix bundle in octane. Nothing says that this should be stable
(say, the helices might dissolve in the octane), but there was an
interesting twist: with a 1.0/1.8 nm cutoff, the bundle does dissolve.
With PME, it doesn't in octane, both simulations were about 4 ns. Not
conclusive, but a bit worrying.
On small-system artefacts with PME: I compared water order inside the
six-helix bundle channel, as this seemed very sensitive to whatever you
change, in a bilayer of about 6.7 nm thickness and in one with 4 nm
extra water. This made no significant difference.
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