[gmx-users] configurations of the two dimensional simulation

Clare evenstar32 at gmail.com
Thu Sep 6 13:34:45 CEST 2012

Dear all,

I'm doing a simulation of the formation of a lipid monolayer, and my system
contains a water layer on the bottom and a layer of the mixture of lipid and
decane on the top. Since I expect the pbc to be only applied to the x and y
direction, I then decide to use the method of "walls". 

However, I'm not sure what exactly is the function of the walls? Do they
prevent the two adjacent boxes from interacting with each other completely? 

Moreover, as mentioned in the manual, if I use "ewald_geometry = 3dc", I can
try to increase the z-dimension of the box, usually by 3 times the dimension
in the z direction. Since the walls are set up in the mdp file which is
applied to the extended box, then I suppose the walls would be located at
the bottom and top of the extended box rather than the original box, aren't
they? in other words, the molecules will go to the extended region of the
box in stead of staying in the original box, am I correct? So do I still
need to extend the box if I'm going to use walls?

Finally, in order to perform the 2 dimensional simulation, do I need to
modify all the mdp files for EM, NVT, NPT and MD, where the "pbc" term is
changed to "pbc=xy" and the options for walls are specified?
I've attached my mdp file for MD below.

Sorry for raising so many questions. Could any one kindly help me with this?
I would very much appreciate it!
Thanks a lot!


title           = Lipid decane and water
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 5000000       ; 2 *5000000 = 50000 ps, 10 ns
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 1000          ; save coordinates every 2 ps
nstvout         = 1000          ; save velocities every 2 ps
nstxtcout       = 1000          ; xtc compressed trajectory output every 2
nstenergy       = 1000          ; save energies every 2 ps
nstlog          = 1000          ; update log file every 2 ps
; Bond parameters
continuation    = yes           ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 10            ; 10 fs
rlist           = 0.9           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 0.9           ; short-range electrostatic cutoff (in nm)
rvdw            = 0.9           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
optimize_fft    = yes           ; optimize at startup for faster long sims
ewald_geometry  = 3dc           ; Ewald sum in 2Ds

; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Lipid   SOL   Decane  ; two coupling groups - more
tau_t           = 0.1     0.1   0.1     ; time constant, in ps
ref_t           = 300     300   300; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
; Periodic boundary conditions
pbc             = xy            ; 2-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off

; walls
nwall           = 2
wall_atomtype   = SOL C10       ;wall at z=0 is formed by water and at
z=z_box is formed by decane
wall_type       = 9-3           ;
;wall_r_linpot  = 0             ;
wall_density    = 33.3679 3.0897; number density of water and decane
wall_ewald_zfac = 3             ;

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