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

[Sergio Garay]

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) Minimization of 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 simulation 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
Facultad de Bioquímica y Cs. Biológicas
Universidad Nacional del Litoral