[gmx-users] Re: Help ! Some molecules go away from my bilayer..... (stearic acid data)

[Sergio Garay]

Dear David:

Stearic acid is a saturated aliphatic carboxylic acid. It has a litle 
head (one carboxylic group) and a long tail with 17 hidrocarbons, with a 
methyl at the end.
The solubility is very low (0.3 mg/100 mL at 20 deg C).
Melting Point: 69.6 deg C
SURFACE TENSION: 28.9 dynes/cm at 70 deg C
There is a paper which made a MD of a bilayer of stearic acid  (P cte - 
isotropic) (Biochim. et Biophys. Acta. 1511 (2001) 156-167).
I made other MD simulations starting from a bilayer configuration not 
obtained with annealing, and in these cases, the stearic acids didn't go 
away from the bilayer.
What shoud I try? Any suggestion ?

Sergio Garay
Biochemist
Facultad de Bioquímica y Cs. Biológicas
Universidad Nacional del Litoral