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

[Baofu Qiao]

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.neale at 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
>