[gmx-users] cutoffs vs pme and lipids
Lynne E. Bilston
l.bilston at unsw.edu.au
Thu Jan 23 01:29:35 CET 2003
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
POWMRI, Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924 Fax: +61-2-9382-2643
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