[gmx-users] wall problem
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.
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
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.
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