[gmx-users] strange empty space inside the system box

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Jan 24 16:59:51 CET 2010

Sounds like a bubble. Do some NpT equilibration by adding pressure  
coupling. That's going to be difficult with your freeze groups though.  
Basically, you need to find a way to get the correct solution density  
between the graphite layers.

-- original message --

Hi all,

Is there anyone who can give me some suggestions?

My system is composed of some polymer chains and waters. The density of
the solution is about 1g/cm^3. Then I added two explicit grahpite layers
(resname=WAL) at the bottom and top of the solution, which are both
freezed in three dimensions in all the simulations. After some
equilibrium runs (about 200ps), there appears a strange space at the
bottom of the solution in the Z direction. For example, the bottom
graphite layer is Z= 0-4nm, Z = 4-6nm is empty (no graphite, no polymer,
no water) , Z=6-30 is the solution, Z=30=34nm is the top graphite layer.
The void space doesn't disappear after 10ns simulation.  Could someone
give me some suggestion?  Thanks a lot in advance!

The following is the .mdp  file. (in the equilibrium run,
coulombtype=cut-off, not PME)

integrator               = md
dt                       = 0.0025
nsteps                   = 8000000
comm-mode                = Linear
nstcomm                  = 1
comm-grps                =

nstlog                   = 800000
nstenergy                = 800000
nstxtcout                = 800000
xtc-precision            = 1000
energygrps               =  WAL

nstlist                      = 10
ns_type                  = grid
rlist                         = 1.2

coulombtype              = pme
rcoulomb                   = 1.2
vdw-type                   = cut-off
rvdw                         = 1.2
DispCorr                   = EnerPres
table-extension           = 1
energygrp_table         =
fourierspacing            = 0.15
pme_order                = 4
ewald_rtol                 = 1e-05
ewald_geometry        = 3d
epsilon_surface          = 0
optimize_fft               = yes

Tcoupl                   = nose-hoover
tc-grps                  = system
tau_t                    = 0.5
ref_t                    = 298

gen_vel                  = yes
gen_temp                 = 298

constraints              = all-bonds

freezegrps               = WAL
freezedim                = Y Y Y
energygrp_excl       = WAL WA

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