[gmx-users] Walls and pressure coupling

[Jingjie]

Dear GMX Users,

 

I am trying to simulate a slab geometry of molecules using 12-6 LJ walls and
pbc=xy. May I know how do I control the pressure of the simulation box? I
have used berendsen semiisotropic and set the pressure to 1 bar, however the
average pressure fluctuates below 0, at a large negative value of -76. The
relevant portions of the .mdp file are reproduced below:

 

; Pressure coupling is on

pcoupl             = berendsen    ; Pressure coupling on in NPT

pcoupltype      = semiisotropic           ; uniform scaling of x-y box
vectors, independent z

tau_p               = 5.0                ; time constant, in ps

ref_p               = 1.0    1.0       ; reference pressure, x-y, z (in bar)

compressibility = 0.0   4.5e-5  ; isothermal compressibility, bar^-1

 

; Periodic boundary conditions

pbc                  = xy                  ; 3-D PBC

 

; Walls on top and bottom

nwall               = 2

wall-atomtype = c c

wall-type         = 12-6

wall-r-linpot    = -1 -1 

wall-ewald-zfac           = 3

ewald-geometry         = 3dc

 

Best Regards,

Jingjie Yeo