[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)
; RUN CONTROL PARAMETERS
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
More information about the gromacs.org_gmx-users
mailing list