[gmx-users] Help!: Some molecules go away from my bilayer.......
sgaray at fbcb.unl.edu.ar
Thu Jul 8 16:20:13 CEST 2004
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
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
Facultad de Bioquímica y Cs. Biológicas
Universidad Nacional del Litoral
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