Hi,
Thanks a lot for the suggestion! NPT does is difficult with the frozen
graphite layers. On the other hand, I have also done another simulation
using the implicit graphite wall with the same polymer solution
(composition and system volume). These implicit wall systems seems good,
at least the empty space is not there. Any other idea about it?
best regards,
Baofu Qiao
chris.ne...@utoronto.ca wrote:
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
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