[gmx-users] cutoffs vs pme and lipids
lindahl at stanford.edu
Thu Jan 23 01:45:06 CET 2003
By "separating", do you mean you get a different area per lipid, or?
In general, lipid systems can be quite pathological :-) Area/lipid is
extremely sensitive to the balance between attractive coulomb forces and
entropy in the chain region, so even small changes can have large
effects (and most forcefields are parameterized using cutoffs for the
There is one significant part of the electrostatics where PME will lead
to a higher area/lipid: All lipid headgroups have a small component of
parallel to the membrane normal. All these parallel dipoles will repell
each other, and with PME we include this effect out to infinity.
does not necessarily mean you always get a higer area/lipid with PME
since there are probably countereffects...
If you want to compare two simulations it is also a good idea to either
use the same VdW cutoff distance, or at least apply dispersion corrections.
Lynne E. Bilston wrote:
> Hi all,
> I'm a little surprised at the quite large differences I get in the
> response of a lipid bilayer when changing from cutoffs to pme. I'm
> simulating a protein/lipid system (POPC), using Peter Tieleman's popc
> files, and the usual lipid corrections to the gromacs forcefield.
> When I use semi-isotropic pressure coupling to apply a pressure to the
> system, I find that there are big differences in how the lipid
> responds. The simulations using cutoffs result in the lipid molecules
> staying together much longer, whereas in the pme simulations, they
> separate much more quickly, and the box expands much faster. this
> makes a really big difference in what the protein sees sitting in the
> membrane. The longer I run the simulation, the more significant the
> difference (at least up to the 10-12ns I've run on the two systems).
> For cutoffs, I'm using rlist, rvdw= 1.0, rcoulomb=1.8, and for pme,
> they're all set to 0.9, based on what I'd read in the list. All other
> parameters stay the same between the two simulations. I've looked at a
> plain lipid system, and see the same thing.
> Is this big difference an expected thing? Are my mdp settings wrong?
> Is there a problem with pme and pressure coupling apart from the
> "artificial ordering in some systems" mentioned in the manual?
> Any ideas/comments/explanations would be welcome.
> Lynne E. Bilston, PhD
> Senior Scientist, Prince of Wales Medical Research Institute, and
> Conjoint Associate Professor, Faculty of Medicine, University of New
> South Wales
> POWMRI, Barker St, Randwick, NSW 2031 Australia
> Tel: +61-2-9382-7924 Fax: +61-2-9382-2643
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