NVT Equilibration problem with interface system

User discussions
1

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
Image460×432 184 KB

2

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.

3

Thanks for your response obZehn. But when I run the NPT equilibration after the NVT I get the “Pressure scaling more than 1%” warning

4

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.

5

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.

6

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.

7

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.

8

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?

9

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?