[gmx-users] Gel Phase in DMPC using Berger force field ??
swolf at bph.rub.de
Mon Dec 10 17:01:52 CET 2007
that problem with the gel phase can come from a lot of issues:
-what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm
twin range cutoff for working properly. Are you using PME for
-how did you set up the pressure coupling?
-900 waters are not really much, the head groups will probably interact
with their mirror images due to pbc. Try a lot more (thought about
10000?) for having a "real" bilayer in a solution.
>From my experience, the Berger lipids are well defined for a specific
temperature, but if you go up/down the temperature scale, they are not
really following the experimental values/phase behaviour. By the way:
experimental data on lipid order parameters varies considerably
throughout the complete literature, so don't rely onto that too much as
Sorry for giving more questions than answers, but that's the shitty part
with lipid bilayers in MD...
> does anyone know whether the Berger force field for DMPC lipids can
> reproduce a gel phase? I didn't really find anything in the
> literature. I sumulated a patch of 128 lipids (with 7 water molecules
> per lipid) at 278 K for 50ns. The lipid chains seem a little more
> ordered than at, say, 300K, but they are not really stretched as one
> would expect in the gel phase.
> Does anyone have experience with that issue? Should I try an even
> lower temperature or less/more water or a larger box? Or is the Berger
> force field not parametrized to reproduce the gel phase at all?
> Thanks at lot,
Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
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