normal polarizable water - vapor causes box to expand in semiisotropic simulation

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2 years 4 months ago - 2 years 4 months ago #9287 by mboy@seas.upenn.edu
Hi all,

I am attempting to use MARTINI to simulate a polyelectrolyte polymer brush using polarizable MARTINI water. It involves using an explicit substrate with position restraints on the substrate and the ends of the polymer brush, and periodic boundary conditions in xyz. I run the following steps:

1) initialize the box using packmol
2) steep energy minimization
3) NVT annealing at 400K to 300K
4) NPT at 300K

Thermostat and barostat settings are shown below:
dt = 0.010
tcoupl = v-rescale
tc-grps = INIT_PMCG PCL_W SUBS
tau_t = 1.0 1.0 1.0
ref_t = 300 300 300
Pcoupl = berendsen
Pcoupltype = semiisotropic ; allows for different pressure in x-y and z directions
tau_p = 6.00 ;
compressibility = 0 3e-4 ; x-y in compressible, compressible in z direction
ref_p = 1.0 1.0 ;

However, when run the NPT step, vapor bubbles of low density seem to form in the polarizable water, and the z dimension of the box keeps expanding until the simulation crashes.

Has anyone seen this issue in membrane or other semi-isotropic pressure simulations? Do you have any suggestions to prevent vapor bubble formation during equilibration?

Any help would be much appreciated!

Thanks,
Mike
Last edit: 2 years 4 months ago by mboy@seas.upenn.edu.

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2 years 4 months ago #9299 by mboy@seas.upenn.edu
Running the first npt simulation at 1000 bar reference pressure, then allowing the pressure to rescale to 1 bar reference pressure eliminated the vapor bubble.

Cheers,
Mike

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2 years 4 months ago #9300 by riccardo
Thanks for following up in your own thread with a solution, Mike!

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