[gmx-users] System shrinkage during vacuum simulation

[Sanim Rahman]

Hello everyone,

I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
slab at the top and bottom of my bilayer system. I equilibrated my system,
tripled the size of my system in the z-direction and then added the 3dc
geometry. My mdp script is written as below:

title = Production MD
; Run parameters
integrator = md
nsteps = 25000000
dt    = 0.002

; Output control
nstxout = 2000
nstvout = 2000
nstxtcout = 2000
nstenergy = 2000
nstlog = 2000

; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4

; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.6
rvdw = 1.6

; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16

; Temperature coupling is on
tcoupl = Nose-Hoover
tc-grps = System
tau_t = 0.2
ref_t = 310

; EWALD/PME/PPPM parameters =
ewald-geometry: 3dc

; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
ref_p = 1.0   1.0
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc    = xyz

; Dispersion correction
DispCorr = EnerPres

; Velocity generation
gen_vel = no

My system shrunk down to a value close to the original dimension in the z
direction as soon as the simulation started after I analyzed it using
g_energy. Is there a mistake with my production .mdp file?

I will truly appreciate your assistance.

Regards,
Sanim Rahman