# Getting lower density and voids inside box during NPT run

**URL:** <https://gromacs.bioexcel.eu/t/getting-lower-density-and-voids-inside-box-during-npt-run/2723>\
**Category:** User discussions\
**Created:** [August 24, 2021, 11:04am UTC](https://gromacs.bioexcel.eu/t/getting-lower-density-and-voids-inside-box-during-npt-run/2723 "2021-08-24T11:04:10Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sikisipra](https://avatars.discourse-cdn.com/v4/letter/s/e9a140/32.png) [@sikisipra](https://gromacs.bioexcel.eu/u/sikisipra)\
**Post date:** [August 24, 2021, 11:04am UTC](https://gromacs.bioexcel.eu/t/getting-lower-density-and-voids-inside-box-during-npt-run/2723/1 "2021-08-24T11:04:10Z")

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GROMACS version:2021.2  
GROMACS modification: No  
Dear Developers and Users,  
I am simulating some polymer chains. I am getting a lower value for density in comparison to experimental density during the NPT run. When I am visualizing the system, there are some voids are there inside the box. How can I remove those empty spaces? I am attaching the mdp file script

integrator = md ; leap-frog integrator  
nsteps = 10000000 ; 10ns  
dt = 0.0001 ; 1 fs  
; Output control  
nstenergy = 10000 ; save energies every 1.0 ps  
nstlog = 10000 ; update log file every 1.0 ps  
nstxout-compressed = 10000 ; save coordinates every 1.0 ps  
; Bond parameters  
continuation = yes ; continuing from NVT  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = h-bonds ; bonds to H are constrained  
lincs\_iter = 1 ; accuracy of LINCS  
lincs\_order = 4 ; also related to accuracy  
; Neighbor searching and vdW  
cutoff-scheme = Verlet  
ns\_type = grid ; search neighboring grid cells  
nstlist = 20 ; largely irrelevant with Verlet  
rlist = 1.2  
vdwtype = cutoff  
vdw-modifier = force-switch  
rvdw-switch = 1.0  
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)  
; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
rcoulomb = 1.2  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
; Temperature coupling  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = system ; two coupling groups - more accurate  
tau\_t = 0.1 ; time constant, in ps  
ref\_t = 425 ; reference temperature, one for each group, in K  
; Pressure coupling  
pcoupl = berendsen;Parrinello-Rahman ; pressure coupling is on for NPT  
pcoupltype = semiisotropic  
; uniform scaling of box vectors  
tau\_p = 1.0 ; time constant, in ps  
ref\_p = 1.0 1.0 ; reference pressure, in bar  
compressibility = 4.5e-5 0.0 ; isothermal compressibility of water, bar^-1  
refcoord\_scaling = com  
; Periodic boundary conditions  
pbc = xyz ; 3-D PBC  
; Dispersion correction is not used for proteins with the C36 additive FF  
DispCorr = EnerPres  
; Velocity generation  
gen\_vel = no ; velocity generation off after NVT

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [August 26, 2021, 10:14am UTC](https://gromacs.bioexcel.eu/t/getting-lower-density-and-voids-inside-box-during-npt-run/2723/2 "2021-08-26T10:14:44Z")

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Hi,

> [@sikisipra](#):
>
> ; Pressure coupling  
> pcoupl = berendsen;Parrinello-Rahman ; pressure coupling is on for NPT  
> pcoupltype = semiisotropic  
> ; uniform scaling of box vectors  
> tau\_p = 1.0 ; time constant, in ps  
> ref\_p = 1.0 1.0 ; reference pressure, in bar  
> compressibility = 4.5e-5 0.0 ;

Just a observation: you couple the pressure in x/y direction while z is kept constant. Is this what you want?  
This setting does not allow to relax z direction and that may be the source of the gaps in the system (just a guess).  
Best regards  
Alessandra