[gmx-users] Help ! Some molecules go away from my bilayer.....

[sgaray at fbcb.unl.edu.ar]

Hi all

I' m simulating a bilayer of stearic acid, using 
ffG96a2x forcefield (I use PBC, integration 
time: 2 fs; Electrostatic: PME; r_coulomg: 15 A, 
r_vdw: 15 A).  I followed this steps:
1)Prepare an initial configuration of 70 
molecules in each layer using adhoc program(37 A 
x 37 A), aprox.: 21 A2 per molecule. Enough SPC 
water to complete a box of 75 A height (distance 
between stearics' heads: 32 A).
2)Minimize the E of the system.  MD without 
restrictions (200 ps, 300 K) with pressure 
coupling (Berendsen) 1 Bar. In order to fit the 
size of the box at P = 1 atm.
3)Annealing (V cte.) with restrictions in the 
stearics'  heads to Z average in each layer ( 
300 K to 370 K, 200 ps) and then (370K to 300K,  
800 ps). In order to break the order of the 
tails.
4)Four MD (300K, 200 ps, coupling pressure: 
Berendsen) reducing the Z restrictions in each 
one til 0 (without restrictions). In order to 
eliminate any force  introduced for the 
restrictions used in the steps before. 
5)MD without restriction (300K, 4ns, pressure 
coupling: Berendsen, tao_p: 4 ps). Always one or 
two stearic acid go away from the bilayer.
6)MD without restriction (300K, 4ns, pressure 
coupling: Berendsen, tao_p: 4ps, surface-
tension: cte). Again, one or two stearic acid go 
away from the bilayer.
7)MD without restriction (300K, 4ns, V cte.).  
Again, one or two stearic acid go away from the 
bilayer.

Is it OK? The stearic's heads are very small, so Is it logical that 
some of them are taken off the membrane due to the water 
interactions?  Any suggestion?  

Sergio Garay
Biochemist
Faculty of Biochemistry and Biological Science
Universidad Nacional del Litoral
Santa Fe (3000). Argentina