normal Water not filling the box (polarizable water)

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9 months 3 weeks ago #8820 by ejohn16
Hi all, I've been attempting to simulate multiple coarse grain monomers in a box of polarizable solvent. Strangely the solvent doesn't appear to be filling the box correctly, after equilibration the solvent clumps together and leaves a large vacuum space and the density graph reflects this.

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I was wondering if anyone else had experienced this problem and had any fixes for it.

The command I used to solvate the box after minimising in vacuum was:

gmx solvate -cp CG_multiple_monomers_minimization_vacuum.gro -cs polarize-water.gro -radius 0.21 -o CG_12_monomers_solvated.gro


The settings for my equilibration mdp file were as follows:

define = -DPOSRES
integrator = md
dt = 0.02
nsteps = 100000
nstcomm = 100

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100


cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 2.5 ; 2.5 (with polarizable water), 16 with default solvent
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau-t = 1.0 1.0
ref-t = 310 310
gen-vel = yes
gen-temp = 310
Pcoupl = berendsen
Pcoupltype = isotropic
tau-p = 2.0
compressibility = 4.5e-5
ref-p = 1.0
refcoord-scaling = com

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9 months 3 weeks ago #8821 by vainikka
Replied by vainikka on topic Water not filling the box (polarizable water)
How does the pressure behave during the equilibration, does your simulation volume increase radically?

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9 months 3 weeks ago #8822 by ejohn16
Replied by ejohn16 on topic Water not filling the box (polarizable water)
The volume actually decreases by quite a bit,

After minimisation:

40.52520 27.01680 27.01680

After equilibration:

33.97602 22.65068 22.65068

In terms of pressure its stable/consistent:

ibb.co/ygGN1XY

The box size decreasing has me wondering if I just need to start with a much bigger box perhaps? Thanks for your reply.

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9 months 3 weeks ago #8823 by vainikka
Replied by vainikka on topic Water not filling the box (polarizable water)
What is your water density before you run the equilibration? Based on your answers, I'd argue that the initial volume is too large.

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