# Water box with a sheet of graphene
**URL:** https://gromacs.bioexcel.eu/t/water-box-with-a-sheet-of-graphene/6285
**Category:** User discussions
**Created:** [April 26, 2023, 1:38pm UTC](https://gromacs.bioexcel.eu/t/water-box-with-a-sheet-of-graphene/6285 "2023-04-26T13:38:17Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@gluizcar](https://gromacs.bioexcel.eu/u/gluizcar)
#### Post date: [April 26, 2023, 1:38pm UTC](https://gromacs.bioexcel.eu/t/water-box-with-a-sheet-of-graphene/6285/1 "2023-04-26T13:38:17Z")
GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
Hello everybody.
I am trying to create a box with a sheet of graphene solvated with H2O, with a size of 17.09 x 25 x 27.13 (angstrom). The system preparation parameters are:
rlis = rcoulomb = rvdw = 0.6
System optimization normally occurs with grompp and mdrun, but the problem is when I use the NPT ensemble. NPT.mdp details:
dt = 0.002
nsteps = 10000
rlis = rcoulomb = rvdw = 0.6
Tcoupl = nose-hoover
Pcoupl = Parrinello-Rahman
pcoupltype = anisotropic
tau\_p = 5.0
compressibility = 0 4.5e-5 0 0 0 0 which would be at 1 atm
ref\_p = 0 1 0 0 0 0
periodic\_molecules = yes
When actually starting the simulation, the error that is reported is the following:
starting mdrun ‘Grephene in Water’
10000 steps, 20.0 feet.
\*\*\* Process received signal \*\*\*
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x55b4ce7797e0
[0] /lib/x86\_64-linux-gnu/libpthread.so.0(+0x14420)[0x7f6511d54420]
\*\*\* End of error message \*\*\*
Segmentation fault (core image recorded)
If I lower the dt to dt = 0.0001:
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or box\_yy-|box\_zy| or box\_zz has become smaller than the cut-off.
Would anyone have an idea how to resolve this issue?
Should I change the barostat to Berendsen?
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### Author:  [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)
#### Post date: [April 28, 2023, 9:46am UTC](https://gromacs.bioexcel.eu/t/water-box-with-a-sheet-of-graphene/6285/2 "2023-04-28T09:46:57Z")
HI,
By ‘optimization’ you mean energy-minimization? Did you get any warning there?
You could try to first run NVT (so constant volume) with dt=0.001 for a few hundred steps, and then switch to NPT (possibly already with dt=0.002). This usually worked out for me.
You could also try to switch thermostat to Berendsen (which I understand to be more stable in case of systems that are initialized far from equilibrium), or C-rescale (was it already implemented in Gromacs 2020? Maybe you want to upgrade to a more recent release.).
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### Author:  [@gluizcar](https://gromacs.bioexcel.eu/u/gluizcar)
#### Post date: [June 4, 2023, 12:58pm UTC](https://gromacs.bioexcel.eu/t/water-box-with-a-sheet-of-graphene/6285/3 "2023-06-04T12:58:36Z")
The problem was on my computer that couldn’t generate the files and had a tracking error. I tried on another computer and it worked. But thanks for the help.