# NVT Equilibration problem with interface system **URL:** \ **Category:** User discussions\ **Created:** [April 18, 2025, 11:26am UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946 "2025-04-18T11:26:21Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Nightwolf](https://avatars.discourse-cdn.com/v4/letter/n/779978/32.png) [@Nightwolf](https://gromacs.bioexcel.eu/u/Nightwolf)\ **Post date:** [April 18, 2025, 11:26am UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/1 "2025-04-18T11:26:21Z")
GROMACS version: GROMACS modification: Yes/No Hello Everyone, I am trying to run an interface system of vacuum/surfactant/water/surfactant/vacuum. The initial energy minimization step is successful, however, when I carryout the NVT equilibration, I observe empty regions formed in the output file. I have tried extending the equilibration time to 20ns but I still observe the same thing. And I only observe this if I place the surfactant at the interface for the same number of molecules and box size. i.e if the surfactants are randomly distributed within the box, the equilibration runs successfully, I have attached an image of the nvt output. Regards. NVT file: title = NVT equilibration define = -DPOSRES ; position restrain Surfactant ; Run parameters integrator = md ; leap-frog integrator nsteps = 20000000 ; 2 \* 20000000 = 40000 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 = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; 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 = 294.15 ; 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 = 294.15 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed ![Image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/619b4c227a9b20b5158096b6a1cd7959f912affa.png) ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [April 18, 2025, 12:41pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/2 "2025-04-18T12:41:12Z")
I would say that this is normal. It’s NVT, so the box is not changing, and once you turn on the dynamics in the NVT the water molecules are going to 'stick’to each other. Usually the solvation steps underestimate the density, that is, the space occupied by water is larger than what it would really be, so when you run dynamics you might have empty bubbles. Just couple the pressure as well to let the volume relax and achieve the correct system density for this temperature. ---
**Author:** ![Nightwolf](https://avatars.discourse-cdn.com/v4/letter/n/779978/32.png) [@Nightwolf](https://gromacs.bioexcel.eu/u/Nightwolf)\ **Post date:** [April 18, 2025, 1:30pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/3 "2025-04-18T13:30:11Z")
Thanks for your response obZehn. But when I run the NPT equilibration after the NVT I get the “Pressure scaling more than 1%” warning ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [April 18, 2025, 1:55pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/4 "2025-04-18T13:55:18Z")
What p-coupling are you using? Try the c-rescale. It probably means that your starting condition is very far from a near equilibrium one. ---
**Author:** ![Nightwolf](https://avatars.discourse-cdn.com/v4/letter/n/779978/32.png) [@Nightwolf](https://gromacs.bioexcel.eu/u/Nightwolf)\ **Post date:** [April 18, 2025, 2:02pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/5 "2025-04-18T14:02:22Z")
I am using c-rescale for the coupling. But I just observed that once I remove the position restraint on the surfactants, the npt equilibration runs successfully. But I want the surfactants to be at the top and the bottom. Because I intend to increase the box size in the z-direction to have a vacuum/surfactant/water setup. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [April 18, 2025, 2:43pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/6 "2025-04-18T14:43:14Z")
But if you restrain them then the volume in between will be frustrated as the water will not relax to a proper equilibrium density. Maybe you will get a better outcome if you first solvate a box of pure water and relax it and then on that you add the surfactant molecules, as the water in between wont have to relax too much (will still have to adapt to the surfactant though). Also eventually I guess you should have the restraints removed anyway? If the molecules are supposed to be phase separated then you shouldn’t enforce the phase separation with energy penalties yourself. ---
**Author:** ![Nightwolf](https://avatars.discourse-cdn.com/v4/letter/n/779978/32.png) [@Nightwolf](https://gromacs.bioexcel.eu/u/Nightwolf)\ **Post date:** [April 18, 2025, 4:15pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/7 "2025-04-18T16:15:24Z")
Thanks obZehn. I think that’s just what I am going to do. I will run a short npt equilibration without the position restraint and then elongate the box for the nvt production run. Thanks again and kind regards. ---
**Author:** ![Nightwolf](https://avatars.discourse-cdn.com/v4/letter/n/779978/32.png) [@Nightwolf](https://gromacs.bioexcel.eu/u/Nightwolf)\ **Post date:** [April 18, 2025, 4:31pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/8 "2025-04-18T16:31:00Z")
Another question though, I was thinking if I can run the npt equilibration without pbc in the z-direction so that the surfactants can still stay close to the edges after the equilbration. This is because I want to maintain the number of molecule on each edge. Is that possible? ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [April 22, 2025, 12:29pm UTC](https://gromacs.bioexcel.eu/t/nvt-equilibration-problem-with-interface-system/11946/9 "2025-04-22T12:29:04Z")
You can try but I do not know how the edges will then react, as having an hard wall will change the local behavior of the molecules. Maybe it is easier if you inserted already the empty space? Of maybe you can first equilibrate the water box alone and then add the surfactants and, at the same time, the empty volume?