[gmx-users] wall problem

Albert mailmd2011 at gmail.com
Tue Feb 4 15:31:44 CET 2014

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 

Hi Justin:

many thanks for your further reply. I am using CHARMM36 FF for the 
simulations. Here is related section of my .mdp file:

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman        ; Pressure coupler used under 
NPT conditions
pcoupltype    = semiisotropic            ; Isotropic scaling in the x-y 
direction, independent of the z direction
tau_p        = 5.0    5.0            ; 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 am using semiistropic for my MD simulations,  shouldn't the 
compressibility sent to zero by default?

thank you very much.

best wishes


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