[gmx-users] box length in z dimension keep increasing when using two walls in NPT ensemble

[Jianguo Li]

Dear all,

I was trying to add two walls at z=0 and z=z_box to my system which contains one 
peptide and one membrane. Since I am interested in how the peptides affect 
membrane properties (i.e., area per lipid), I need to use semi-isotropic 
pressure coupling. But I wanted to mimick the two-dimensional periodicity of the 
membrane and thus don't want to include the z-component of the ewald summation, 
so I decided to add two walls so that I can use ewald_geometry=3dc. Since there 
is no periodicity in z dimension, I kept two regions up and below the membrane 
neutral. However, when the simulation proceeds, the box length in z dimemsion 
keep increasing and results in a large vacum between image boxes in z dimension. 
Could anyone help me figure out what's going wrong? The following is my mdp file 
and I will be glad to provide any other details if needed:

cpp = /usr/bin/cpp
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100000000 ;.
nstxout = 50000 ; 
nstxtcout = 1000
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 1000
nstlist = 5
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = Nose-Hoover
tc-grps = Protein lipid SOL_Ion
tau_t = 0.5  0.5  0.5           
ref_t = 310  310  310
;Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = semiisotropic         ; uniform scaling of x-y box vectors, 
independent z
tau_p           = 1.0 1.0                       ; time constant, in ps
ref_p           = 1.0 1.0             ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5  4.5e-5  ; isothermal compressibility, bar^-1

gen_vel = no
gen_temp = 310.0
gen_seed = 173529

nstcomm         = 5
comm-mode       = Linear
comm-grps       = Protein_lipid SOL_Ion
; put two walls
pbc     = xy
ewald_geometry  =   3dc
nwall         =      2
wall_atomtype   =  C  C
wall_type       =  12-6
wall_ewald_zfac =  3
wall_r_linpot   = 0.5

Thanks very much!

Cheers,

Jianguo
Postdoc,
BII&SERI,
Singapore

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