[gmx-users] wall problem

Albert mailmd2011 at gmail.com
Tue Feb 4 16:59:49 CET 2014

Hello Justin:

I took your advices and submit the system to MD simulations. After NVT, 
the vacuum layer was still there. However, my pbc box shrinked to its 
orginal size after NPT, and the vacuum layer was disapeared.... here is 
my compreasiblity settings:

; Pressure coupling parameters
pcoupl        = berendsen        ; Pressure coupler used under NPT 
pcoupltype    = semiisotropic            ; Isotropic scaling in the x-y 
direction, independent of the z direction
tau_p        = 1.0    1.0            ; Coupling time constant (ps)
ref_p        = 1.0    1.0            ; Reference pressure for coupling, 
x-y, z directions (bar)
compressibility = 4.5e-5    4.5e-5        ; Isothermal compressibility 

I enlarged the vacuum layer in each leaflet around 3nm.

thank you very much.


On 02/04/2014 02:50 PM, Justin Lemkul wrote:
> Elongate the box in the z-dimension and set its compressibility to 
> zero in the .mdp file.  This issue was discussed at length just a few 
> days ago.  Beware possible ordering artifacts of the interfaces.
> -Justin

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