# Make solvent box **URL:** \ **Category:** User discussions\ **Created:** [August 19, 2021, 9:47pm UTC](https://gromacs.bioexcel.eu/t/make-solvent-box/2704 "2021-08-19T21:47:02Z")\ **Posts on this page:** 3\ **Page:** 1

**Author:** ![l454025801](https://avatars.discourse-cdn.com/v4/letter/l/50afbb/32.png) [@l454025801](https://gromacs.bioexcel.eu/u/l454025801)\ **Post date:** [August 19, 2021, 9:47pm UTC](https://gromacs.bioexcel.eu/t/make-solvent-box/2704/1 "2021-08-19T21:47:02Z")

GROMACS version: 20 Hi I am trying to make a DMSO solvent box. I followed the guide to make a box of 1.96 x 1.96 x 1.96 nm with 64 DMSO molecules (density = 1.1 g/cm3). EM and NVT equlibration is fine. However, if I use the solvent with other molecules, the system will expand (box size increases). Then I tried NPT simulation on the DMSO solvents only. The box will expand as well. All files are attached below. Thank you! _ **EM** _ ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.5 ; Short-range electrostatic cut-off rvdw = 0.5 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions _ **NVT** _ title = OPLS Lysozyme NVT equilibration define = ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 \* 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 0.5 ; short-range electrostatic cutoff (in nm) rvdw = 0.5 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau\_t = 0.1 ; time constant, in ps ref\_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 300 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed _ **NPT** _ title = OPLS Lysozyme NPT equilibration define = ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 \* 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 0.5 ; short-range electrostatic cutoff (in nm) rvdw = 0.5 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau\_t = 0.1 ; time constant, in ps ref\_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant, in ps ref\_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord\_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen\_vel = no ; Velocity generation is off ---

**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 20, 2021, 7:54am UTC](https://gromacs.bioexcel.eu/t/make-solvent-box/2704/2 "2021-08-20T07:54:24Z")

Hi, The current NPT setting uses water compressibility values. DMSO may have different compressibility. You can try to calculate DMSO model compressibility and use it in the DMSO box equilibration. Maybe this post can help > [@How to determine compressibility?](https://gromacs.bioexcel.eu/t/how-to-determine-compressibility/787): > > GROMACS version:2020.2 GROMACS modification: Yes/No Dear all, I am trying to run an npt calculation for a pure organic solvent system. How to determine the compressibility then? Many thanks in advance. Best Alessandra ---

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [August 20, 2021, 5:26pm UTC](https://gromacs.bioexcel.eu/t/make-solvent-box/2704/3 "2021-08-20T17:26:13Z")

Your box size is incredibly small and the cutoffs are very short, so you are also likely getting inaccuracy in the LJ potential. You don’t say what the parent force field is, but at 0.5 nm, there is still considerable LJ interaction that you’re cutting off and leaving to a long-range correction, which is not appropriate. Build a bigger box (better statistics, smaller fluctuations) and use a sensible cutoff.